VAPr.tests package

Submodules

VAPr.tests.test_annovar_output_parsing module

class VAPr.tests.test_annovar_output_parsing.TestAnnovarAnnotatedVariant(methodName='runTest')[source]

Bases: unittest.case.TestCase

test__list_has_valid_content_false_all_none()[source]
test__list_has_valid_content_false_empty()[source]
test__list_has_valid_content_true()[source]
test__make_per_sample_annotation_dict_maximum_content()[source]

Ensure that if info exists in the format string for all relevant fields, it is put into the dictionary.

test__make_per_sample_annotation_dict_minimum_content()[source]

Ensure that if info isn’t in the format string for relevant fields, a minimal dictionary is made.

test__make_per_sample_annotation_dict_none()[source]

Ensure that if input genotype fields string doesn’t contain any real info, None is returned.

test_make_per_variant_annotation_dict()[source]
class VAPr.tests.test_annovar_output_parsing.TestAnnovarTxtParser(methodName='runTest')[source]

Bases: unittest.case.TestCase

ANNOVAR_ANNOTATION_CONTENT = 'Chr\tStart\tEnd\tRef\tAlt\tFunc.knownGene\tGene.knownGene\tGeneDetail.knownGene\tExonicFunc.knownGene\tAAChange.knownGene\ttfbsConsSites\tcytoBand\ttargetScanS\tgenomicSuperDups\tesp6500siv2_all\t1000g2015aug_all\tPopFreqMax\t1000G_ALL\t1000G_AFR\t1000G_AMR\t1000G_EAS\t1000G_EUR\t1000G_SAS\tExAC_ALL\tExAC_AFR\tExAC_AMR\tExAC_EAS\tExAC_FIN\tExAC_NFE\tExAC_OTH\tExAC_SAS\tESP6500siv2_ALL\tESP6500siv2_AA\tESP6500siv2_EA\tCG46\tCLINSIG\tCLNDBN\tCLNACC\tCLNDSDB\tCLNDSDBID\tcosmic70\tnci60\tOtherinfo\nchrM\t516\t517\tCA\t-\tupstream\tDQ582201,JB137816\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t43.70\t2\tchrM\t515\t.\tGCA\tG\t43.70\t.\tAC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.85;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:80,6,0\t./.:0,0\nchrM\t1890\t1890\tG\tA\tncRNA_exonic\tTVAS5\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t56.74\t2\tchrM\t1890\t.\tG\tA\t56.74\t.\tAC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=43.64;MQ0=0;QD=28.37;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:84,6,0\t./.:0,0\nchrM\t6262\t6262\tG\tA\tncRNA_exonic\tBC018860\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t185.90\t5\tchrM\t6262\t.\tG\tA\t185.90\t.\tAC=2;AF=1.00;AN=2;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.97;SOR=1.981\tGT:AD:DP:GQ:PL\t1/1:0,5:5:15:214,15,0\t./.:0,0\nchrM\t8698\t8698\tG\tA\tncRNA_exonic\tOK/SW-cl.16\t.\t.\t.\tScore=908;Name=V$FOXD3_01\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t107.28\t3\tchrM\t8698\t.\tG\tA\t107.28\t.\tAC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.57;MQ0=0;QD=26.82;SOR=1.179\tGT:AD:DP:GQ:PL\t1/1:0,3:3:9:135,9,0\t./.:0,0\nchrM\t146\t146\tT\tC\tupstream;downstream\tJB137816;DQ582201\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t62.74\t2\tchrM\t146\trs370482130\tT\tC\t62.74\t.\tAC=2;AF=1.00;AN=2;DB;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.91;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:90,6,0\t./.:0,0\nchrM\t150\t150\tT\tC\tupstream;downstream\tJB137816;DQ582201\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t62.74\t2\tchrM\t150\t.\tT\tC\t62.74\t.\tAC=2;AF=1.00;AN=2;DP=3;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=20.91;SOR=0.693\tGT:AD:DP:GQ:PL\t./.:0,0\t1/1:0,2:2:6:90,6,0\nchr1\t195\t195\tC\tT\tupstream;downstream\tJB137816;DQ582201\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t61.74\t2\tchrM\t195\t.\tC\tT\t61.74\t.\tAC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.87;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:89,6,0\t1/1:0,3:3:9:135,9,0\nchrM\t410\t410\tA\tT\tupstream\tDQ582201,JB137816\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t62.74\t2\tchrM\t410\t.\tA\tT\t62.74\t.\tAC=2;AF=1.00;AN=2;DP=2;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.37;SOR=0.693\tGT:AD:DP:GQ:PL\t./.:0,0\t./.:0,0\nchr2\t626\t626\tG\tA\tncRNA_exonic\tBC018860\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t185.90\t5\tchrM\t6262\t.\tG\tA\t185.90\t.\tAC=2;AF=1.00;AN=2;DP=5;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.97;SOR=1.981\tGT:AD:DP:GQ:PL\t1/1:0,5:5:15:214,15,0\t./.:0,0\nchr4\t698\t698\tG\tA\tncRNA_exonic\tOK/SW-cl.16\t.\t.\t.\tScore=908;Name=V$FOXD3_01\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t1\t107.28\t3\tchrM\t8698\t.\tG\tA\t107.28\t.\tAC=2;AF=1.00;AN=2;DP=4;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=49.57;MQ0=0;QD=26.82;SOR=1.179\tGT:AD:DP:GQ:PL\t1/1:0,3:3:9:135,9,0\t./.:0,0\n'
test__normalize_header()[source]
test__parse_single_variant_record()[source]
test__parse_to_dict_with_score_key()[source]
test__rewrite_value_if_special_header_chrom_cleaned()[source]
test__rewrite_value_if_special_header_chrom_unchanged()[source]
test__rewrite_value_if_special_header_to_dict_w_score()[source]
test__rewrite_value_if_special_header_to_float()[source]
test__rewrite_value_if_special_header_to_int()[source]
test__rewrite_value_if_special_header_unchanged()[source]
test_read_chunk_of_annotations_to_dicts_list()[source]

VAPr.tests.test_annovar_running module

class VAPr.tests.test_annovar_running.TestAnnovarWrapper(methodName='runTest')[source]

Bases: unittest.case.TestCase

classmethod setUpClass()[source]

Hook method for setting up class fixture before running tests in the class.

test__build_annovar_database_download_command_str()[source]
test__build_table_annovar_command_str()[source]
test__get_annovar_dbs_to_use_for_build_version_error()[source]
test__get_annovar_dbs_to_use_for_build_version_hg19()[source]
test__get_annovar_dbs_to_use_for_build_version_hg38()[source]

VAPr.tests.test_chunk_processing module

class VAPr.tests.test_chunk_processing.TestAnnotationJobParamsIndices(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_get_num_possible_indices()[source]
class VAPr.tests.test_chunk_processing.TestFunctions(methodName='runTest')[source]

Bases: unittest.case.TestCase

test__collect_chunk_annotations_no_sample_info()[source]
test__collect_chunk_annotations_with_sample_info()[source]
test__get_hgvs_ids_from_vcf()[source]
test__get_myvariantinfo_annotations_dict()[source]
test__get_myvariantinfo_annotations_dict_fatal_error_immediately()[source]
test__merge_annovar_and_myvariant_dicts()[source]
test__merge_annovar_and_myvariant_dicts_error()[source]
test__remove_unwanted_keys()[source]

VAPr.tests.test_filtering module

class VAPr.tests.test_filtering.TestFunctions(methodName='runTest')[source]

Bases: unittest.case.TestCase

test__append_sample_id_constraint_if_needed_is_needed()[source]
test__append_sample_id_constraint_if_needed_is_not_needed()[source]
test_get_any_of_sample_ids_filter()[source]
test_get_sample_id_filter()[source]
test_make_de_novo_variants_filter()[source]
test_make_deleterious_compound_heterozygote_variants_filter_w_samples()[source]
test_make_deleterious_compound_heterozygote_variants_filter_wo_samples()[source]
test_make_known_disease_variants_filter_w_samples()[source]
test_make_known_disease_variants_filter_wo_samples()[source]
test_make_rare_deleterious_variants_filter_w_samples()[source]
test_make_rare_deleterious_variants_filter_wo_samples()[source]

VAPr.tests.test_validation module

This module exposes unit-tests of validation.py functionality.

class VAPr.tests.test_validation.TestFunctions(methodName='runTest')[source]

Bases: unittest.case.TestCase

Test top-level functions of validation.py module.

test_convert_to_nonneg_int_fail_negative()[source]

Test that a non-null, negative integer input raises an error for either nullable value.

test_convert_to_nonneg_int_fail_negative_non_integer()[source]

Test that a non-null, negative non-integer input raises an error for either nullable value.

test_convert_to_nonneg_int_not_integer()[source]

Test that a non-null, non-integer input raises an error for either nullable value.

test_convert_to_nonneg_int_not_nullable_pass()[source]

Test that a non-null, non-negative-integer-castable input produces cast output for either nullable value.

test_convert_to_nonneg_int_nullable_fail()[source]

Test that a null input raises an error when nullable=False.

test_convert_to_nonneg_int_nullable_pass_null()[source]

Test that a null input produces output of utilities.database.NULL when nullable=True.

test_convert_to_nullable_not_null()[source]

Test that a castable non-null input produces a cast output.

test_convert_to_nullable_not_null_error()[source]

Test that a non-castable non-null error raises an error.

test_convert_to_nullable_null()[source]

Test that a null input (‘.’) produces output of None.

VAPr.tests.test_vapr_core module

class VAPr.tests.test_vapr_core.TestVaprAnnotator(methodName='runTest')[source]

Bases: unittest.case.TestCase

test___init__single_bzipped_file()[source]
test__get_num_lines_in_file()[source]
test__get_validated_genome_version()[source]
test__get_validated_genome_version_default()[source]
test__get_validated_genome_version_error()[source]
test__make_jobs_params_tuples_list_no_samples_default_verbose()[source]
test__make_jobs_params_tuples_list_no_samples_default_verbose_less_than_chunk()[source]
test__make_jobs_params_tuples_list_samples_with_verbose()[source]
test__make_merged_vcf_w_design_file()[source]
test__make_merged_vcf_wo_design_file()[source]
class VAPr.tests.test_vapr_core.TestVaprDataset(methodName='runTest')[source]

Bases: unittest.case.TestCase

classmethod setUpClass()[source]

Hook method for setting up class fixture before running tests in the class.

test__get_filtered_variants_by_sample_all()[source]
test__get_filtered_variants_by_sample_single()[source]
test__get_filtered_variants_by_sample_some()[source]
test__warn_if_no_output_false()[source]
test__warn_if_no_output_true()[source]
test__write_annotated_csv()[source]
test__write_annotated_vcf()[source]
test_de_novo_variants()[source]
test_deleterious_compound_heterozygous_variants_all_samples()[source]
test_deleterious_compound_heterozygous_variants_specific_samples()[source]
test_get_all_variants()[source]
test_get_custom_filtered_variants()[source]
test_get_custom_filtered_variants_empty_db()[source]
test_get_distinct_sample_ids()[source]
test_get_variants_as_dataframe_all()[source]
test_get_variants_as_dataframe_some()[source]
test_get_variants_for_sample()[source]
test_get_variants_for_samples()[source]
test_known_disease_variants_all_samples()[source]
test_known_disease_variants_specific_samples()[source]
test_rare_deleterious_variants_all_samples()[source]
test_rare_deleterious_variants_specific_samples()[source]
VAPr.tests.test_vapr_core.help_make_filter(sample_names=None)[source]

VAPr.tests.test_vcf_genotype_fields_parsing module

class VAPr.tests.test_vcf_genotype_fields_parsing.TestAllele(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_read_counts_setter()[source]
test_read_counts_setter_error()[source]
class VAPr.tests.test_vcf_genotype_fields_parsing.TestFunctions(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_fill_filtered_reads_count()[source]
test_fill_genotype()[source]
test_fill_genotype_confidence()[source]
test_fill_genotype_likelihoods_no_alleles()[source]
test_fill_genotype_likelihoods_three_alleles()[source]
test_fill_genotype_likelihoods_warn_too_few_likelihoods_1()[source]
test_fill_genotype_likelihoods_warn_too_few_likelihoods_2()[source]
test_fill_genotype_likelihoods_warn_too_many_alleles_implied()[source]
test_fill_genotype_warn()[source]
test_fill_unfiltered_reads_counts()[source]
test_fill_unfiltered_reads_counts_warn()[source]
class VAPr.tests.test_vcf_genotype_fields_parsing.TestGenotypeLikelihood(methodName='runTest')[source]

Bases: unittest.case.TestCase

test__validate_allele_relationship_fail()[source]
test__validate_allele_relationship_pass()[source]
test_allele1_number_setter()[source]
test_allele1_number_setter_error()[source]
test_allele2_number_setter()[source]
test_allele2_number_setter_error()[source]
test_genotype_confidence_setter_error()[source]
test_likelihood_neg_exponent_setter()[source]
class VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeInfo(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_filter_passing_reads_count_setter()[source]
test_filter_passing_reads_count_setter_error()[source]
test_genotype_confidence_setter()[source]
test_genotype_confidence_setter_error()[source]
class VAPr.tests.test_vcf_genotype_fields_parsing.TestVCFGenotypeString(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_is_valid_genotype_fields_string_false_delimited()[source]
test_is_valid_genotype_fields_string_false_period()[source]
test_is_valid_genotype_fields_string_true()[source]
test_parse_GT_AD_DP_GQ_PL()[source]
test_parse_GT_GQ_PL()[source]
test_parse_error_reported_as_warn()[source]

VAPr.tests.test_vcf_merging module

class VAPr.tests.test_vcf_merging.TestFunctions(methodName='runTest')[source]

Bases: unittest.case.TestCase

HG00096_VCF_CONTENTS = '##fileformat=VCFv4.1\n##FILTER=<ID=PASS,Description="All filters passed">\n##fileDate=20150218\n##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz\n##source=1000GenomesPhase3Pipeline\n##contig=<ID=1,assembly=b37,length=249250621>\n##contig=<ID=2,assembly=b37,length=243199373>\n##contig=<ID=3,assembly=b37,length=198022430>\n##contig=<ID=4,assembly=b37,length=191154276>\n##contig=<ID=5,assembly=b37,length=180915260>\n##contig=<ID=6,assembly=b37,length=171115067>\n##contig=<ID=7,assembly=b37,length=159138663>\n##contig=<ID=8,assembly=b37,length=146364022>\n##contig=<ID=9,assembly=b37,length=141213431>\n##contig=<ID=10,assembly=b37,length=135534747>\n##contig=<ID=11,assembly=b37,length=135006516>\n##contig=<ID=12,assembly=b37,length=133851895>\n##contig=<ID=13,assembly=b37,length=115169878>\n##contig=<ID=14,assembly=b37,length=107349540>\n##contig=<ID=15,assembly=b37,length=102531392>\n##contig=<ID=16,assembly=b37,length=90354753>\n##contig=<ID=17,assembly=b37,length=81195210>\n##contig=<ID=18,assembly=b37,length=78077248>\n##contig=<ID=19,assembly=b37,length=59128983>\n##contig=<ID=20,assembly=b37,length=63025520>\n##contig=<ID=21,assembly=b37,length=48129895>\n##contig=<ID=22,assembly=b37,length=51304566>\n##contig=<ID=GL000191.1,assembly=b37,length=106433>\n##contig=<ID=GL000192.1,assembly=b37,length=547496>\n##contig=<ID=GL000193.1,assembly=b37,length=189789>\n##contig=<ID=GL000194.1,assembly=b37,length=191469>\n##contig=<ID=GL000195.1,assembly=b37,length=182896>\n##contig=<ID=GL000196.1,assembly=b37,length=38914>\n##contig=<ID=GL000197.1,assembly=b37,length=37175>\n##contig=<ID=GL000198.1,assembly=b37,length=90085>\n##contig=<ID=GL000199.1,assembly=b37,length=169874>\n##contig=<ID=GL000200.1,assembly=b37,length=187035>\n##contig=<ID=GL000201.1,assembly=b37,length=36148>\n##contig=<ID=GL000202.1,assembly=b37,length=40103>\n##contig=<ID=GL000203.1,assembly=b37,length=37498>\n##contig=<ID=GL000204.1,assembly=b37,length=81310>\n##contig=<ID=GL000205.1,assembly=b37,length=174588>\n##contig=<ID=GL000206.1,assembly=b37,length=41001>\n##contig=<ID=GL000207.1,assembly=b37,length=4262>\n##contig=<ID=GL000208.1,assembly=b37,length=92689>\n##contig=<ID=GL000209.1,assembly=b37,length=159169>\n##contig=<ID=GL000210.1,assembly=b37,length=27682>\n##contig=<ID=GL000211.1,assembly=b37,length=166566>\n##contig=<ID=GL000212.1,assembly=b37,length=186858>\n##contig=<ID=GL000213.1,assembly=b37,length=164239>\n##contig=<ID=GL000214.1,assembly=b37,length=137718>\n##contig=<ID=GL000215.1,assembly=b37,length=172545>\n##contig=<ID=GL000216.1,assembly=b37,length=172294>\n##contig=<ID=GL000217.1,assembly=b37,length=172149>\n##contig=<ID=GL000218.1,assembly=b37,length=161147>\n##contig=<ID=GL000219.1,assembly=b37,length=179198>\n##contig=<ID=GL000220.1,assembly=b37,length=161802>\n##contig=<ID=GL000221.1,assembly=b37,length=155397>\n##contig=<ID=GL000222.1,assembly=b37,length=186861>\n##contig=<ID=GL000223.1,assembly=b37,length=180455>\n##contig=<ID=GL000224.1,assembly=b37,length=179693>\n##contig=<ID=GL000225.1,assembly=b37,length=211173>\n##contig=<ID=GL000226.1,assembly=b37,length=15008>\n##contig=<ID=GL000227.1,assembly=b37,length=128374>\n##contig=<ID=GL000228.1,assembly=b37,length=129120>\n##contig=<ID=GL000229.1,assembly=b37,length=19913>\n##contig=<ID=GL000230.1,assembly=b37,length=43691>\n##contig=<ID=GL000231.1,assembly=b37,length=27386>\n##contig=<ID=GL000232.1,assembly=b37,length=40652>\n##contig=<ID=GL000233.1,assembly=b37,length=45941>\n##contig=<ID=GL000234.1,assembly=b37,length=40531>\n##contig=<ID=GL000235.1,assembly=b37,length=34474>\n##contig=<ID=GL000236.1,assembly=b37,length=41934>\n##contig=<ID=GL000237.1,assembly=b37,length=45867>\n##contig=<ID=GL000238.1,assembly=b37,length=39939>\n##contig=<ID=GL000239.1,assembly=b37,length=33824>\n##contig=<ID=GL000240.1,assembly=b37,length=41933>\n##contig=<ID=GL000241.1,assembly=b37,length=42152>\n##contig=<ID=GL000242.1,assembly=b37,length=43523>\n##contig=<ID=GL000243.1,assembly=b37,length=43341>\n##contig=<ID=GL000244.1,assembly=b37,length=39929>\n##contig=<ID=GL000245.1,assembly=b37,length=36651>\n##contig=<ID=GL000246.1,assembly=b37,length=38154>\n##contig=<ID=GL000247.1,assembly=b37,length=36422>\n##contig=<ID=GL000248.1,assembly=b37,length=39786>\n##contig=<ID=GL000249.1,assembly=b37,length=38502>\n##contig=<ID=MT,assembly=b37,length=16569>\n##contig=<ID=NC_007605,assembly=b37,length=171823>\n##contig=<ID=X,assembly=b37,length=155270560>\n##contig=<ID=Y,assembly=b37,length=59373566>\n##contig=<ID=hs37d5,assembly=b37,length=35477943>\n##ALT=<ID=CNV,Description="Copy Number Polymorphism">\n##ALT=<ID=DEL,Description="Deletion">\n##ALT=<ID=DUP,Description="Duplication">\n##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">\n##ALT=<ID=INS:ME:LINE1,Description="Insertion of LINE1 element">\n##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">\n##ALT=<ID=INS:MT,Description="Nuclear Mitochondrial Insertion">\n##ALT=<ID=INV,Description="Inversion">\n##ALT=<ID=CN0,Description="Copy number allele: 0 copies">\n##ALT=<ID=CN1,Description="Copy number allele: 1 copy">\n##ALT=<ID=CN2,Description="Copy number allele: 2 copies">\n##ALT=<ID=CN3,Description="Copy number allele: 3 copies">\n##ALT=<ID=CN4,Description="Copy number allele: 4 copies">\n##ALT=<ID=CN5,Description="Copy number allele: 5 copies">\n##ALT=<ID=CN6,Description="Copy number allele: 6 copies">\n##ALT=<ID=CN7,Description="Copy number allele: 7 copies">\n##ALT=<ID=CN8,Description="Copy number allele: 8 copies">\n##ALT=<ID=CN9,Description="Copy number allele: 9 copies">\n##ALT=<ID=CN10,Description="Copy number allele: 10 copies">\n##ALT=<ID=CN11,Description="Copy number allele: 11 copies">\n##ALT=<ID=CN12,Description="Copy number allele: 12 copies">\n##ALT=<ID=CN13,Description="Copy number allele: 13 copies">\n##ALT=<ID=CN14,Description="Copy number allele: 14 copies">\n##ALT=<ID=CN15,Description="Copy number allele: 15 copies">\n##ALT=<ID=CN16,Description="Copy number allele: 16 copies">\n##ALT=<ID=CN17,Description="Copy number allele: 17 copies">\n##ALT=<ID=CN18,Description="Copy number allele: 18 copies">\n##ALT=<ID=CN19,Description="Copy number allele: 19 copies">\n##ALT=<ID=CN20,Description="Copy number allele: 20 copies">\n##ALT=<ID=CN21,Description="Copy number allele: 21 copies">\n##ALT=<ID=CN22,Description="Copy number allele: 22 copies">\n##ALT=<ID=CN23,Description="Copy number allele: 23 copies">\n##ALT=<ID=CN24,Description="Copy number allele: 24 copies">\n##ALT=<ID=CN25,Description="Copy number allele: 25 copies">\n##ALT=<ID=CN26,Description="Copy number allele: 26 copies">\n##ALT=<ID=CN27,Description="Copy number allele: 27 copies">\n##ALT=<ID=CN28,Description="Copy number allele: 28 copies">\n##ALT=<ID=CN29,Description="Copy number allele: 29 copies">\n##ALT=<ID=CN30,Description="Copy number allele: 30 copies">\n##ALT=<ID=CN31,Description="Copy number allele: 31 copies">\n##ALT=<ID=CN32,Description="Copy number allele: 32 copies">\n##ALT=<ID=CN33,Description="Copy number allele: 33 copies">\n##ALT=<ID=CN34,Description="Copy number allele: 34 copies">\n##ALT=<ID=CN35,Description="Copy number allele: 35 copies">\n##ALT=<ID=CN36,Description="Copy number allele: 36 copies">\n##ALT=<ID=CN37,Description="Copy number allele: 37 copies">\n##ALT=<ID=CN38,Description="Copy number allele: 38 copies">\n##ALT=<ID=CN39,Description="Copy number allele: 39 copies">\n##ALT=<ID=CN40,Description="Copy number allele: 40 copies">\n##ALT=<ID=CN41,Description="Copy number allele: 41 copies">\n##ALT=<ID=CN42,Description="Copy number allele: 42 copies">\n##ALT=<ID=CN43,Description="Copy number allele: 43 copies">\n##ALT=<ID=CN44,Description="Copy number allele: 44 copies">\n##ALT=<ID=CN45,Description="Copy number allele: 45 copies">\n##ALT=<ID=CN46,Description="Copy number allele: 46 copies">\n##ALT=<ID=CN47,Description="Copy number allele: 47 copies">\n##ALT=<ID=CN48,Description="Copy number allele: 48 copies">\n##ALT=<ID=CN49,Description="Copy number allele: 49 copies">\n##ALT=<ID=CN50,Description="Copy number allele: 50 copies">\n##ALT=<ID=CN51,Description="Copy number allele: 51 copies">\n##ALT=<ID=CN52,Description="Copy number allele: 52 copies">\n##ALT=<ID=CN53,Description="Copy number allele: 53 copies">\n##ALT=<ID=CN54,Description="Copy number allele: 54 copies">\n##ALT=<ID=CN55,Description="Copy number allele: 55 copies">\n##ALT=<ID=CN56,Description="Copy number allele: 56 copies">\n##ALT=<ID=CN57,Description="Copy number allele: 57 copies">\n##ALT=<ID=CN58,Description="Copy number allele: 58 copies">\n##ALT=<ID=CN59,Description="Copy number allele: 59 copies">\n##ALT=<ID=CN60,Description="Copy number allele: 60 copies">\n##ALT=<ID=CN61,Description="Copy number allele: 61 copies">\n##ALT=<ID=CN62,Description="Copy number allele: 62 copies">\n##ALT=<ID=CN63,Description="Copy number allele: 63 copies">\n##ALT=<ID=CN64,Description="Copy number allele: 64 copies">\n##ALT=<ID=CN65,Description="Copy number allele: 65 copies">\n##ALT=<ID=CN66,Description="Copy number allele: 66 copies">\n##ALT=<ID=CN67,Description="Copy number allele: 67 copies">\n##ALT=<ID=CN68,Description="Copy number allele: 68 copies">\n##ALT=<ID=CN69,Description="Copy number allele: 69 copies">\n##ALT=<ID=CN70,Description="Copy number allele: 70 copies">\n##ALT=<ID=CN71,Description="Copy number allele: 71 copies">\n##ALT=<ID=CN72,Description="Copy number allele: 72 copies">\n##ALT=<ID=CN73,Description="Copy number allele: 73 copies">\n##ALT=<ID=CN74,Description="Copy number allele: 74 copies">\n##ALT=<ID=CN75,Description="Copy number allele: 75 copies">\n##ALT=<ID=CN76,Description="Copy number allele: 76 copies">\n##ALT=<ID=CN77,Description="Copy number allele: 77 copies">\n##ALT=<ID=CN78,Description="Copy number allele: 78 copies">\n##ALT=<ID=CN79,Description="Copy number allele: 79 copies">\n##ALT=<ID=CN80,Description="Copy number allele: 80 copies">\n##ALT=<ID=CN81,Description="Copy number allele: 81 copies">\n##ALT=<ID=CN82,Description="Copy number allele: 82 copies">\n##ALT=<ID=CN83,Description="Copy number allele: 83 copies">\n##ALT=<ID=CN84,Description="Copy number allele: 84 copies">\n##ALT=<ID=CN85,Description="Copy number allele: 85 copies">\n##ALT=<ID=CN86,Description="Copy number allele: 86 copies">\n##ALT=<ID=CN87,Description="Copy number allele: 87 copies">\n##ALT=<ID=CN88,Description="Copy number allele: 88 copies">\n##ALT=<ID=CN89,Description="Copy number allele: 89 copies">\n##ALT=<ID=CN90,Description="Copy number allele: 90 copies">\n##ALT=<ID=CN91,Description="Copy number allele: 91 copies">\n##ALT=<ID=CN92,Description="Copy number allele: 92 copies">\n##ALT=<ID=CN93,Description="Copy number allele: 93 copies">\n##ALT=<ID=CN94,Description="Copy number allele: 94 copies">\n##ALT=<ID=CN95,Description="Copy number allele: 95 copies">\n##ALT=<ID=CN96,Description="Copy number allele: 96 copies">\n##ALT=<ID=CN97,Description="Copy number allele: 97 copies">\n##ALT=<ID=CN98,Description="Copy number allele: 98 copies">\n##ALT=<ID=CN99,Description="Copy number allele: 99 copies">\n##ALT=<ID=CN100,Description="Copy number allele: 100 copies">\n##ALT=<ID=CN101,Description="Copy number allele: 101 copies">\n##ALT=<ID=CN102,Description="Copy number allele: 102 copies">\n##ALT=<ID=CN103,Description="Copy number allele: 103 copies">\n##ALT=<ID=CN104,Description="Copy number allele: 104 copies">\n##ALT=<ID=CN105,Description="Copy number allele: 105 copies">\n##ALT=<ID=CN106,Description="Copy number allele: 106 copies">\n##ALT=<ID=CN107,Description="Copy number allele: 107 copies">\n##ALT=<ID=CN108,Description="Copy number allele: 108 copies">\n##ALT=<ID=CN109,Description="Copy number allele: 109 copies">\n##ALT=<ID=CN110,Description="Copy number allele: 110 copies">\n##ALT=<ID=CN111,Description="Copy number allele: 111 copies">\n##ALT=<ID=CN112,Description="Copy number allele: 112 copies">\n##ALT=<ID=CN113,Description="Copy number allele: 113 copies">\n##ALT=<ID=CN114,Description="Copy number allele: 114 copies">\n##ALT=<ID=CN115,Description="Copy number allele: 115 copies">\n##ALT=<ID=CN116,Description="Copy number allele: 116 copies">\n##ALT=<ID=CN117,Description="Copy number allele: 117 copies">\n##ALT=<ID=CN118,Description="Copy number allele: 118 copies">\n##ALT=<ID=CN119,Description="Copy number allele: 119 copies">\n##ALT=<ID=CN120,Description="Copy number allele: 120 copies">\n##ALT=<ID=CN121,Description="Copy number allele: 121 copies">\n##ALT=<ID=CN122,Description="Copy number allele: 122 copies">\n##ALT=<ID=CN123,Description="Copy number allele: 123 copies">\n##ALT=<ID=CN124,Description="Copy number allele: 124 copies">\n##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n##INFO=<ID=CS,Number=1,Type=String,Description="Source call set.">\n##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">\n##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n##INFO=<ID=MC,Number=.,Type=String,Description="Merged calls.">\n##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END<POLARITY; If there is only 5\' OR 3\' support for this call, will be NULL NULL for START and END">\n##INFO=<ID=MEND,Number=1,Type=Integer,Description="Mitochondrial end coordinate of inserted sequence">\n##INFO=<ID=MLEN,Number=1,Type=Integer,Description="Estimated length of mitochondrial insert">\n##INFO=<ID=MSTART,Number=1,Type=Integer,Description="Mitochondrial start coordinate of inserted sequence">\n##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="SV length. It is only calculated for structural variation MEIs. For other types of SVs; one may calculate the SV length by INFO:END-START+1, or by finding the difference between lengthes of REF and ALT alleles">\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n##INFO=<ID=TSD,Number=1,Type=String,Description="Precise Target Site Duplication for bases, if unknown, value will be NULL">\n##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1)">\n##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n##INFO=<ID=EAS_AF,Number=A,Type=Float,Description="Allele frequency in the EAS populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=EUR_AF,Number=A,Type=Float,Description="Allele frequency in the EUR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=AFR_AF,Number=A,Type=Float,Description="Allele frequency in the AFR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=AMR_AF,Number=A,Type=Float,Description="Allele frequency in the AMR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=SAS_AF,Number=A,Type=Float,Description="Allele frequency in the SAS populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth; only low coverage data were counted towards the DP, exome data were not used">\n##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele. Format: AA|REF|ALT|IndelType. AA: Ancestral allele, REF:Reference Allele, ALT:Alternate Allele, IndelType:Type of Indel (REF, ALT and IndelType are only defined for indels)">\n##INFO=<ID=VT,Number=.,Type=String,Description="indicates what type of variant the line represents">\n##INFO=<ID=EX_TARGET,Number=0,Type=Flag,Description="indicates whether a variant is within the exon pull down target boundaries">\n##INFO=<ID=MULTI_ALLELIC,Number=0,Type=Flag,Description="indicates whether a site is multi-allelic">\n##bcftools_viewVersion=1.6+htslib-1.6\n##bcftools_viewCommand=view -c1 -Oz -s HG00096 -o G1000_chr1_10000_20000.HG00096.vcf.gz G1000_chr1_10000_20000.vcf.gz; Date=Mon Nov 6 15:48:17 2017\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00096\n1\t10177\trs367896724\tA\tAC\t100\tPASS\tAC=1;AF=0.425319;AN=2;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE);VT=INDEL\tGT\t1|0\n1\t10352\trs555500075\tT\tTA\t100\tPASS\tAC=1;AF=0.4375;AN=2;NS=2504;DP=88915;EAS_AF=0.4306;AMR_AF=0.4107;AFR_AF=0.4788;EUR_AF=0.4264;SAS_AF=0.4192;AA=|||unknown(NO_COVERAGE);VT=INDEL\tGT\t1|0\n1\t10616\trs376342519\tCCGCCGTTGCAAAGGCGCGCCG\tC\t100\tPASS\tAC=2;AF=0.993011;AN=2;NS=2504;DP=2365;EAS_AF=0.9911;AMR_AF=0.9957;AFR_AF=0.9894;EUR_AF=0.994;SAS_AF=0.9969;VT=INDEL\tGT\t1|1\n1\t14464\trs546169444\tA\tT\t100\tPASS\tAC=2;AF=0.0958466;AN=2;NS=2504;DP=26761;EAS_AF=0.005;AMR_AF=0.1138;AFR_AF=0.0144;EUR_AF=0.1859;SAS_AF=0.1943;AA=a|||;VT=SNP\tGT\t1|1\n1\t14930\trs75454623\tA\tG\t100\tPASS\tAC=1;AF=0.482228;AN=2;NS=2504;DP=42231;EAS_AF=0.4137;AMR_AF=0.5231;AFR_AF=0.4811;EUR_AF=0.5209;SAS_AF=0.4857;AA=a|||;VT=SNP\tGT\t1|0\n1\t15211\trs78601809\tT\tG\t100\tPASS\tAC=1;AF=0.609026;AN=2;NS=2504;DP=32245;EAS_AF=0.504;AMR_AF=0.6772;AFR_AF=0.5371;EUR_AF=0.7316;SAS_AF=0.6401;AA=t|||;VT=SNP\tGT\t0|1\n1\t15274\trs62636497\tA\tG,T\t100\tPASS\tAC=1,1;AF=0.347244,0.640974;AN=2;NS=2504;DP=23255;EAS_AF=0.4812,0.5188;AMR_AF=0.2752,0.7205;AFR_AF=0.323,0.6369;EUR_AF=0.2922,0.7078;SAS_AF=0.3497,0.6472;AA=g|||;VT=SNP;MULTI_ALLELIC\tGT\t1|2\n1\t15820\trs2691315\tG\tT\t100\tPASS\tAC=1;AF=0.410543;AN=2;NS=2504;DP=14933;EAS_AF=0.6052;AMR_AF=0.2939;AFR_AF=0.4849;EUR_AF=0.2714;SAS_AF=0.3354;AA=t|||;VT=SNP;EX_TARGET\tGT\t1|0\n1\t15903\trs557514207\tG\tGC\t100\tPASS\tAC=1;AF=0.441094;AN=2;NS=2504;DP=7012;EAS_AF=0.8681;AMR_AF=0.415;AFR_AF=0.0431;EUR_AF=0.4652;SAS_AF=0.5327;AA=ccc|CC|CCC|deletion;VT=INDEL;EX_TARGET\tGT\t0|1\n1\t18849\trs533090414\tC\tG\t100\tPASS\tAC=2;AF=0.951877;AN=2;NS=2504;DP=4700;EAS_AF=1;AMR_AF=0.9769;AFR_AF=0.8411;EUR_AF=0.9911;SAS_AF=0.9939;AA=g|||;VT=SNP\tGT\t1|1\n'
HG00097_VCF_CONTENTS = '##fileformat=VCFv4.1\n##FILTER=<ID=PASS,Description="All filters passed">\n##fileDate=20150218\n##reference=ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz\n##source=1000GenomesPhase3Pipeline\n##contig=<ID=1,assembly=b37,length=249250621>\n##contig=<ID=2,assembly=b37,length=243199373>\n##contig=<ID=3,assembly=b37,length=198022430>\n##contig=<ID=4,assembly=b37,length=191154276>\n##contig=<ID=5,assembly=b37,length=180915260>\n##contig=<ID=6,assembly=b37,length=171115067>\n##contig=<ID=7,assembly=b37,length=159138663>\n##contig=<ID=8,assembly=b37,length=146364022>\n##contig=<ID=9,assembly=b37,length=141213431>\n##contig=<ID=10,assembly=b37,length=135534747>\n##contig=<ID=11,assembly=b37,length=135006516>\n##contig=<ID=12,assembly=b37,length=133851895>\n##contig=<ID=13,assembly=b37,length=115169878>\n##contig=<ID=14,assembly=b37,length=107349540>\n##contig=<ID=15,assembly=b37,length=102531392>\n##contig=<ID=16,assembly=b37,length=90354753>\n##contig=<ID=17,assembly=b37,length=81195210>\n##contig=<ID=18,assembly=b37,length=78077248>\n##contig=<ID=19,assembly=b37,length=59128983>\n##contig=<ID=20,assembly=b37,length=63025520>\n##contig=<ID=21,assembly=b37,length=48129895>\n##contig=<ID=22,assembly=b37,length=51304566>\n##contig=<ID=GL000191.1,assembly=b37,length=106433>\n##contig=<ID=GL000192.1,assembly=b37,length=547496>\n##contig=<ID=GL000193.1,assembly=b37,length=189789>\n##contig=<ID=GL000194.1,assembly=b37,length=191469>\n##contig=<ID=GL000195.1,assembly=b37,length=182896>\n##contig=<ID=GL000196.1,assembly=b37,length=38914>\n##contig=<ID=GL000197.1,assembly=b37,length=37175>\n##contig=<ID=GL000198.1,assembly=b37,length=90085>\n##contig=<ID=GL000199.1,assembly=b37,length=169874>\n##contig=<ID=GL000200.1,assembly=b37,length=187035>\n##contig=<ID=GL000201.1,assembly=b37,length=36148>\n##contig=<ID=GL000202.1,assembly=b37,length=40103>\n##contig=<ID=GL000203.1,assembly=b37,length=37498>\n##contig=<ID=GL000204.1,assembly=b37,length=81310>\n##contig=<ID=GL000205.1,assembly=b37,length=174588>\n##contig=<ID=GL000206.1,assembly=b37,length=41001>\n##contig=<ID=GL000207.1,assembly=b37,length=4262>\n##contig=<ID=GL000208.1,assembly=b37,length=92689>\n##contig=<ID=GL000209.1,assembly=b37,length=159169>\n##contig=<ID=GL000210.1,assembly=b37,length=27682>\n##contig=<ID=GL000211.1,assembly=b37,length=166566>\n##contig=<ID=GL000212.1,assembly=b37,length=186858>\n##contig=<ID=GL000213.1,assembly=b37,length=164239>\n##contig=<ID=GL000214.1,assembly=b37,length=137718>\n##contig=<ID=GL000215.1,assembly=b37,length=172545>\n##contig=<ID=GL000216.1,assembly=b37,length=172294>\n##contig=<ID=GL000217.1,assembly=b37,length=172149>\n##contig=<ID=GL000218.1,assembly=b37,length=161147>\n##contig=<ID=GL000219.1,assembly=b37,length=179198>\n##contig=<ID=GL000220.1,assembly=b37,length=161802>\n##contig=<ID=GL000221.1,assembly=b37,length=155397>\n##contig=<ID=GL000222.1,assembly=b37,length=186861>\n##contig=<ID=GL000223.1,assembly=b37,length=180455>\n##contig=<ID=GL000224.1,assembly=b37,length=179693>\n##contig=<ID=GL000225.1,assembly=b37,length=211173>\n##contig=<ID=GL000226.1,assembly=b37,length=15008>\n##contig=<ID=GL000227.1,assembly=b37,length=128374>\n##contig=<ID=GL000228.1,assembly=b37,length=129120>\n##contig=<ID=GL000229.1,assembly=b37,length=19913>\n##contig=<ID=GL000230.1,assembly=b37,length=43691>\n##contig=<ID=GL000231.1,assembly=b37,length=27386>\n##contig=<ID=GL000232.1,assembly=b37,length=40652>\n##contig=<ID=GL000233.1,assembly=b37,length=45941>\n##contig=<ID=GL000234.1,assembly=b37,length=40531>\n##contig=<ID=GL000235.1,assembly=b37,length=34474>\n##contig=<ID=GL000236.1,assembly=b37,length=41934>\n##contig=<ID=GL000237.1,assembly=b37,length=45867>\n##contig=<ID=GL000238.1,assembly=b37,length=39939>\n##contig=<ID=GL000239.1,assembly=b37,length=33824>\n##contig=<ID=GL000240.1,assembly=b37,length=41933>\n##contig=<ID=GL000241.1,assembly=b37,length=42152>\n##contig=<ID=GL000242.1,assembly=b37,length=43523>\n##contig=<ID=GL000243.1,assembly=b37,length=43341>\n##contig=<ID=GL000244.1,assembly=b37,length=39929>\n##contig=<ID=GL000245.1,assembly=b37,length=36651>\n##contig=<ID=GL000246.1,assembly=b37,length=38154>\n##contig=<ID=GL000247.1,assembly=b37,length=36422>\n##contig=<ID=GL000248.1,assembly=b37,length=39786>\n##contig=<ID=GL000249.1,assembly=b37,length=38502>\n##contig=<ID=MT,assembly=b37,length=16569>\n##contig=<ID=NC_007605,assembly=b37,length=171823>\n##contig=<ID=X,assembly=b37,length=155270560>\n##contig=<ID=Y,assembly=b37,length=59373566>\n##contig=<ID=hs37d5,assembly=b37,length=35477943>\n##ALT=<ID=CNV,Description="Copy Number Polymorphism">\n##ALT=<ID=DEL,Description="Deletion">\n##ALT=<ID=DUP,Description="Duplication">\n##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">\n##ALT=<ID=INS:ME:LINE1,Description="Insertion of LINE1 element">\n##ALT=<ID=INS:ME:SVA,Description="Insertion of SVA element">\n##ALT=<ID=INS:MT,Description="Nuclear Mitochondrial Insertion">\n##ALT=<ID=INV,Description="Inversion">\n##ALT=<ID=CN0,Description="Copy number allele: 0 copies">\n##ALT=<ID=CN1,Description="Copy number allele: 1 copy">\n##ALT=<ID=CN2,Description="Copy number allele: 2 copies">\n##ALT=<ID=CN3,Description="Copy number allele: 3 copies">\n##ALT=<ID=CN4,Description="Copy number allele: 4 copies">\n##ALT=<ID=CN5,Description="Copy number allele: 5 copies">\n##ALT=<ID=CN6,Description="Copy number allele: 6 copies">\n##ALT=<ID=CN7,Description="Copy number allele: 7 copies">\n##ALT=<ID=CN8,Description="Copy number allele: 8 copies">\n##ALT=<ID=CN9,Description="Copy number allele: 9 copies">\n##ALT=<ID=CN10,Description="Copy number allele: 10 copies">\n##ALT=<ID=CN11,Description="Copy number allele: 11 copies">\n##ALT=<ID=CN12,Description="Copy number allele: 12 copies">\n##ALT=<ID=CN13,Description="Copy number allele: 13 copies">\n##ALT=<ID=CN14,Description="Copy number allele: 14 copies">\n##ALT=<ID=CN15,Description="Copy number allele: 15 copies">\n##ALT=<ID=CN16,Description="Copy number allele: 16 copies">\n##ALT=<ID=CN17,Description="Copy number allele: 17 copies">\n##ALT=<ID=CN18,Description="Copy number allele: 18 copies">\n##ALT=<ID=CN19,Description="Copy number allele: 19 copies">\n##ALT=<ID=CN20,Description="Copy number allele: 20 copies">\n##ALT=<ID=CN21,Description="Copy number allele: 21 copies">\n##ALT=<ID=CN22,Description="Copy number allele: 22 copies">\n##ALT=<ID=CN23,Description="Copy number allele: 23 copies">\n##ALT=<ID=CN24,Description="Copy number allele: 24 copies">\n##ALT=<ID=CN25,Description="Copy number allele: 25 copies">\n##ALT=<ID=CN26,Description="Copy number allele: 26 copies">\n##ALT=<ID=CN27,Description="Copy number allele: 27 copies">\n##ALT=<ID=CN28,Description="Copy number allele: 28 copies">\n##ALT=<ID=CN29,Description="Copy number allele: 29 copies">\n##ALT=<ID=CN30,Description="Copy number allele: 30 copies">\n##ALT=<ID=CN31,Description="Copy number allele: 31 copies">\n##ALT=<ID=CN32,Description="Copy number allele: 32 copies">\n##ALT=<ID=CN33,Description="Copy number allele: 33 copies">\n##ALT=<ID=CN34,Description="Copy number allele: 34 copies">\n##ALT=<ID=CN35,Description="Copy number allele: 35 copies">\n##ALT=<ID=CN36,Description="Copy number allele: 36 copies">\n##ALT=<ID=CN37,Description="Copy number allele: 37 copies">\n##ALT=<ID=CN38,Description="Copy number allele: 38 copies">\n##ALT=<ID=CN39,Description="Copy number allele: 39 copies">\n##ALT=<ID=CN40,Description="Copy number allele: 40 copies">\n##ALT=<ID=CN41,Description="Copy number allele: 41 copies">\n##ALT=<ID=CN42,Description="Copy number allele: 42 copies">\n##ALT=<ID=CN43,Description="Copy number allele: 43 copies">\n##ALT=<ID=CN44,Description="Copy number allele: 44 copies">\n##ALT=<ID=CN45,Description="Copy number allele: 45 copies">\n##ALT=<ID=CN46,Description="Copy number allele: 46 copies">\n##ALT=<ID=CN47,Description="Copy number allele: 47 copies">\n##ALT=<ID=CN48,Description="Copy number allele: 48 copies">\n##ALT=<ID=CN49,Description="Copy number allele: 49 copies">\n##ALT=<ID=CN50,Description="Copy number allele: 50 copies">\n##ALT=<ID=CN51,Description="Copy number allele: 51 copies">\n##ALT=<ID=CN52,Description="Copy number allele: 52 copies">\n##ALT=<ID=CN53,Description="Copy number allele: 53 copies">\n##ALT=<ID=CN54,Description="Copy number allele: 54 copies">\n##ALT=<ID=CN55,Description="Copy number allele: 55 copies">\n##ALT=<ID=CN56,Description="Copy number allele: 56 copies">\n##ALT=<ID=CN57,Description="Copy number allele: 57 copies">\n##ALT=<ID=CN58,Description="Copy number allele: 58 copies">\n##ALT=<ID=CN59,Description="Copy number allele: 59 copies">\n##ALT=<ID=CN60,Description="Copy number allele: 60 copies">\n##ALT=<ID=CN61,Description="Copy number allele: 61 copies">\n##ALT=<ID=CN62,Description="Copy number allele: 62 copies">\n##ALT=<ID=CN63,Description="Copy number allele: 63 copies">\n##ALT=<ID=CN64,Description="Copy number allele: 64 copies">\n##ALT=<ID=CN65,Description="Copy number allele: 65 copies">\n##ALT=<ID=CN66,Description="Copy number allele: 66 copies">\n##ALT=<ID=CN67,Description="Copy number allele: 67 copies">\n##ALT=<ID=CN68,Description="Copy number allele: 68 copies">\n##ALT=<ID=CN69,Description="Copy number allele: 69 copies">\n##ALT=<ID=CN70,Description="Copy number allele: 70 copies">\n##ALT=<ID=CN71,Description="Copy number allele: 71 copies">\n##ALT=<ID=CN72,Description="Copy number allele: 72 copies">\n##ALT=<ID=CN73,Description="Copy number allele: 73 copies">\n##ALT=<ID=CN74,Description="Copy number allele: 74 copies">\n##ALT=<ID=CN75,Description="Copy number allele: 75 copies">\n##ALT=<ID=CN76,Description="Copy number allele: 76 copies">\n##ALT=<ID=CN77,Description="Copy number allele: 77 copies">\n##ALT=<ID=CN78,Description="Copy number allele: 78 copies">\n##ALT=<ID=CN79,Description="Copy number allele: 79 copies">\n##ALT=<ID=CN80,Description="Copy number allele: 80 copies">\n##ALT=<ID=CN81,Description="Copy number allele: 81 copies">\n##ALT=<ID=CN82,Description="Copy number allele: 82 copies">\n##ALT=<ID=CN83,Description="Copy number allele: 83 copies">\n##ALT=<ID=CN84,Description="Copy number allele: 84 copies">\n##ALT=<ID=CN85,Description="Copy number allele: 85 copies">\n##ALT=<ID=CN86,Description="Copy number allele: 86 copies">\n##ALT=<ID=CN87,Description="Copy number allele: 87 copies">\n##ALT=<ID=CN88,Description="Copy number allele: 88 copies">\n##ALT=<ID=CN89,Description="Copy number allele: 89 copies">\n##ALT=<ID=CN90,Description="Copy number allele: 90 copies">\n##ALT=<ID=CN91,Description="Copy number allele: 91 copies">\n##ALT=<ID=CN92,Description="Copy number allele: 92 copies">\n##ALT=<ID=CN93,Description="Copy number allele: 93 copies">\n##ALT=<ID=CN94,Description="Copy number allele: 94 copies">\n##ALT=<ID=CN95,Description="Copy number allele: 95 copies">\n##ALT=<ID=CN96,Description="Copy number allele: 96 copies">\n##ALT=<ID=CN97,Description="Copy number allele: 97 copies">\n##ALT=<ID=CN98,Description="Copy number allele: 98 copies">\n##ALT=<ID=CN99,Description="Copy number allele: 99 copies">\n##ALT=<ID=CN100,Description="Copy number allele: 100 copies">\n##ALT=<ID=CN101,Description="Copy number allele: 101 copies">\n##ALT=<ID=CN102,Description="Copy number allele: 102 copies">\n##ALT=<ID=CN103,Description="Copy number allele: 103 copies">\n##ALT=<ID=CN104,Description="Copy number allele: 104 copies">\n##ALT=<ID=CN105,Description="Copy number allele: 105 copies">\n##ALT=<ID=CN106,Description="Copy number allele: 106 copies">\n##ALT=<ID=CN107,Description="Copy number allele: 107 copies">\n##ALT=<ID=CN108,Description="Copy number allele: 108 copies">\n##ALT=<ID=CN109,Description="Copy number allele: 109 copies">\n##ALT=<ID=CN110,Description="Copy number allele: 110 copies">\n##ALT=<ID=CN111,Description="Copy number allele: 111 copies">\n##ALT=<ID=CN112,Description="Copy number allele: 112 copies">\n##ALT=<ID=CN113,Description="Copy number allele: 113 copies">\n##ALT=<ID=CN114,Description="Copy number allele: 114 copies">\n##ALT=<ID=CN115,Description="Copy number allele: 115 copies">\n##ALT=<ID=CN116,Description="Copy number allele: 116 copies">\n##ALT=<ID=CN117,Description="Copy number allele: 117 copies">\n##ALT=<ID=CN118,Description="Copy number allele: 118 copies">\n##ALT=<ID=CN119,Description="Copy number allele: 119 copies">\n##ALT=<ID=CN120,Description="Copy number allele: 120 copies">\n##ALT=<ID=CN121,Description="Copy number allele: 121 copies">\n##ALT=<ID=CN122,Description="Copy number allele: 122 copies">\n##ALT=<ID=CN123,Description="Copy number allele: 123 copies">\n##ALT=<ID=CN124,Description="Copy number allele: 124 copies">\n##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">\n##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">\n##INFO=<ID=CS,Number=1,Type=String,Description="Source call set.">\n##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of this variant">\n##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">\n##INFO=<ID=MC,Number=.,Type=String,Description="Merged calls.">\n##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END<POLARITY; If there is only 5\' OR 3\' support for this call, will be NULL NULL for START and END">\n##INFO=<ID=MEND,Number=1,Type=Integer,Description="Mitochondrial end coordinate of inserted sequence">\n##INFO=<ID=MLEN,Number=1,Type=Integer,Description="Estimated length of mitochondrial insert">\n##INFO=<ID=MSTART,Number=1,Type=Integer,Description="Mitochondrial start coordinate of inserted sequence">\n##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="SV length. It is only calculated for structural variation MEIs. For other types of SVs; one may calculate the SV length by INFO:END-START+1, or by finding the difference between lengthes of REF and ALT alleles">\n##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">\n##INFO=<ID=TSD,Number=1,Type=String,Description="Precise Target Site Duplication for bases, if unknown, value will be NULL">\n##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">\n##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1)">\n##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">\n##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n##INFO=<ID=EAS_AF,Number=A,Type=Float,Description="Allele frequency in the EAS populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=EUR_AF,Number=A,Type=Float,Description="Allele frequency in the EUR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=AFR_AF,Number=A,Type=Float,Description="Allele frequency in the AFR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=AMR_AF,Number=A,Type=Float,Description="Allele frequency in the AMR populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=SAS_AF,Number=A,Type=Float,Description="Allele frequency in the SAS populations calculated from AC and AN, in the range (0,1)">\n##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth; only low coverage data were counted towards the DP, exome data were not used">\n##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele. Format: AA|REF|ALT|IndelType. AA: Ancestral allele, REF:Reference Allele, ALT:Alternate Allele, IndelType:Type of Indel (REF, ALT and IndelType are only defined for indels)">\n##INFO=<ID=VT,Number=.,Type=String,Description="indicates what type of variant the line represents">\n##INFO=<ID=EX_TARGET,Number=0,Type=Flag,Description="indicates whether a variant is within the exon pull down target boundaries">\n##INFO=<ID=MULTI_ALLELIC,Number=0,Type=Flag,Description="indicates whether a site is multi-allelic">\n##bcftools_viewVersion=1.6+htslib-1.6\n##bcftools_viewCommand=view -c1 -Oz -s HG00097 -o G1000_chr1_10000_20000.HG00097.vcf.gz G1000_chr1_10000_20000.vcf.gz; Date=Mon Nov 6 15:48:23 2017\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00097\n1\t10177\trs367896724\tA\tAC\t100\tPASS\tAC=1;AF=0.425319;AN=2;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE);VT=INDEL\tGT\t0|1\n1\t10352\trs555500075\tT\tTA\t100\tPASS\tAC=1;AF=0.4375;AN=2;NS=2504;DP=88915;EAS_AF=0.4306;AMR_AF=0.4107;AFR_AF=0.4788;EUR_AF=0.4264;SAS_AF=0.4192;AA=|||unknown(NO_COVERAGE);VT=INDEL\tGT\t1|0\n1\t10616\trs376342519\tCCGCCGTTGCAAAGGCGCGCCG\tC\t100\tPASS\tAC=2;AF=0.993011;AN=2;NS=2504;DP=2365;EAS_AF=0.9911;AMR_AF=0.9957;AFR_AF=0.9894;EUR_AF=0.994;SAS_AF=0.9969;VT=INDEL\tGT\t1|1\n1\t13110\trs540538026\tG\tA\t100\tPASS\tAC=1;AF=0.0267572;AN=2;NS=2504;DP=23422;EAS_AF=0.002;AMR_AF=0.036;AFR_AF=0.0053;EUR_AF=0.0567;SAS_AF=0.044;AA=g|||;VT=SNP\tGT\t1|0\n1\t13116\trs62635286\tT\tG\t100\tPASS\tAC=1;AF=0.0970447;AN=2;NS=2504;DP=22340;EAS_AF=0.0248;AMR_AF=0.121;AFR_AF=0.0295;EUR_AF=0.1869;SAS_AF=0.1534;AA=t|||;VT=SNP\tGT\t1|0\n1\t13118\trs200579949\tA\tG\t100\tPASS\tAC=1;AF=0.0970447;AN=2;NS=2504;DP=21395;EAS_AF=0.0248;AMR_AF=0.121;AFR_AF=0.0295;EUR_AF=0.1869;SAS_AF=0.1534;AA=a|||;VT=SNP\tGT\t1|0\n1\t14599\trs531646671\tT\tA\t100\tPASS\tAC=1;AF=0.147564;AN=2;NS=2504;DP=32081;EAS_AF=0.0893;AMR_AF=0.1758;AFR_AF=0.121;EUR_AF=0.161;SAS_AF=0.2096;AA=t|||;VT=SNP\tGT\t0|1\n1\t14604\trs541940975\tA\tG\t100\tPASS\tAC=1;AF=0.147564;AN=2;NS=2504;DP=29231;EAS_AF=0.0893;AMR_AF=0.1758;AFR_AF=0.121;EUR_AF=0.161;SAS_AF=0.2096;AA=a|||;VT=SNP\tGT\t0|1\n1\t14930\trs75454623\tA\tG\t100\tPASS\tAC=1;AF=0.482228;AN=2;NS=2504;DP=42231;EAS_AF=0.4137;AMR_AF=0.5231;AFR_AF=0.4811;EUR_AF=0.5209;SAS_AF=0.4857;AA=a|||;VT=SNP\tGT\t0|1\n1\t15211\trs78601809\tT\tG\t100\tPASS\tAC=1;AF=0.609026;AN=2;NS=2504;DP=32245;EAS_AF=0.504;AMR_AF=0.6772;AFR_AF=0.5371;EUR_AF=0.7316;SAS_AF=0.6401;AA=t|||;VT=SNP\tGT\t0|1\n1\t15274\trs62636497\tA\tG,T\t100\tPASS\tAC=0,2;AF=0.347244,0.640974;AN=2;NS=2504;DP=23255;EAS_AF=0.4812,0.5188;AMR_AF=0.2752,0.7205;AFR_AF=0.323,0.6369;EUR_AF=0.2922,0.7078;SAS_AF=0.3497,0.6472;AA=g|||;VT=SNP;MULTI_ALLELIC\tGT\t2|2\n1\t15820\trs2691315\tG\tT\t100\tPASS\tAC=1;AF=0.410543;AN=2;NS=2504;DP=14933;EAS_AF=0.6052;AMR_AF=0.2939;AFR_AF=0.4849;EUR_AF=0.2714;SAS_AF=0.3354;AA=t|||;VT=SNP;EX_TARGET\tGT\t0|1\n1\t15903\trs557514207\tG\tGC\t100\tPASS\tAC=1;AF=0.441094;AN=2;NS=2504;DP=7012;EAS_AF=0.8681;AMR_AF=0.415;AFR_AF=0.0431;EUR_AF=0.4652;SAS_AF=0.5327;AA=ccc|CC|CCC|deletion;VT=INDEL;EX_TARGET\tGT\t0|1\n1\t18849\trs533090414\tC\tG\t100\tPASS\tAC=2;AF=0.951877;AN=2;NS=2504;DP=4700;EAS_AF=1;AMR_AF=0.9769;AFR_AF=0.8411;EUR_AF=0.9911;SAS_AF=0.9939;AA=g|||;VT=SNP\tGT\t1|1\n'
classmethod setUpClass()[source]

Hook method for setting up class fixture before running tests in the class.

test__build_bgzip_vcf_command_str()[source]
test__build_index_vcf_command_str()[source]
test__build_merge_vcf_command_str()[source]
test__get_vcf_file_paths_list_in_directory()[source]
test__get_vcf_file_paths_list_in_directory_none()[source]
test__merge_bgzipped_indexed_vcfs()[source]
test_bgzip_and_index_vcf_is_vcf_gz()[source]
test_bgzip_and_index_vcf_not_vcf_gz()[source]
test_merge_vcfs_by_dir_error_no_files_found_bgzipped()[source]
test_merge_vcfs_by_dir_error_no_files_found_not_bgzipped()[source]
test_merge_vcfs_by_list_error_no_files_found()[source]
test_merge_vcfs_multiple_by_dir_bgzipped()[source]
test_merge_vcfs_multiple_by_dir_not_bgzipped()[source]
test_merge_vcfs_multiple_by_list()[source]
test_merge_vcfs_single_already_bgzipped()[source]
test_merge_vcfs_single_by_dir()[source]
test_merge_vcfs_single_by_list()[source]
test_merge_vcfs_single_no_copy_needed()[source]
VAPr.tests.test_vcf_merging.help_get_test_file_info()[source]

Module contents