diff --git a/src/test/resources/ArCompoundTests.tsv b/src/test/resources/ArCompoundTests.tsv index fcac998..818f876 100644 --- a/src/test/resources/ArCompoundTests.tsv +++ b/src/test/resources/ArCompoundTests.tsv @@ -26,4 +26,7 @@ multiallelic2 2/2 0/1 AFFECTED MALE 0/1 0/0 UNAFFECTED 0/0 1/0 UNAFFECTED 0/0 0/ multiallelic3 2/4 0/1 AFFECTED MALE 0/1 0/0 UNAFFECTED 0/0 1/0 UNAFFECTED 0/0 0/0 UNAFFECTED possible multiallelic4 2/4 0/1 AFFECTED MALE 4/4 0/1 AFFECTED 0/0 1/0 UNAFFECTED 0/0 0/0 UNAFFECTED false FatherIsHom1 1/0 0/1 AFFECTED MALE 1/1 0/1 UNAFFECTED 0/1 0/0 UNAFFECTED false -FatherIsHom2 1/0 0/1 AFFECTED MALE 1/1 0/0 UNAFFECTED 0/1 0/0 UNAFFECTED false \ No newline at end of file +FatherIsHom2 1/0 0/1 AFFECTED MALE 1/1 0/0 UNAFFECTED 0/1 0/0 UNAFFECTED false +regular_switched 1/0 1/0 AFFECTED MALE 0/0 1/0 UNAFFECTED 1/0 0/0 UNAFFECTED true +regularBrotherMissingFromVcf_switched 1/0 1/0 AFFECTED MALE 0/0 0/1 UNAFFECTED 0/1 0/0 UNAFFECTED UNAFFECTED possible +regular_switched 1/0 0/1 AFFECTED MALE 0/0 1/0 UNAFFECTED 1/0 0/0 UNAFFECTED true \ No newline at end of file diff --git a/src/test/resources/expected_noParents.vcf b/src/test/resources/expected_noParents.vcf index 745124f..8b8857e 100644 --- a/src/test/resources/expected_noParents.vcf +++ b/src/test/resources/expected_noParents.vcf @@ -41,30 +41,30 @@ ##contig= ##fileDate=20200320 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Mother Father Patient2 Mother2 Father2 -1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2:1 0/0:50 0/0:50 1/0:50:AD_IP:::ID2:1 0/0:50 1/0:50 -1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::::0 1/1:50 0/1:50 1/0:50:AD::::0 1/1:50 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID1,ID2:1 0/1:50 0/1:50 1/0:50:AD:::ID2:1 1/0:50 0/0:50 -1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::::0 1/0:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 +1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2:1 0/0:50 0/0:50 1/0:50:AD_IP,AR_C:1_123459_C_G::ID1,ID2:1 0/0:50 1/0:50 +1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:1_123460_C_G::ID3 ./.:50 0/0:50 1/0:50:AD,AR_C:1_123459_C_G,1_123460_C_G::ID3:1 1/0:50 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::::0 1/1:50 0/1:50 1/0:50:AD,AR_C:1_123458_C_G,1_123460_C_G::ID3:1 1/1:50 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID1,ID2:1 0/1:50 0/1:50 1/0:50:AD,AR_C:1_123457_C_G::ID1,ID2:1 1/0:50 0/0:50 +1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:1_123458_C_G::ID3:1 1/0:50 0/0:50 1/0:50:AD,AR_C:1_123458_C_G,1_123459_C_G::ID3:1 1/0:50 0/0:50 1 123461 . C G . PASS CSQ=P|1|G|GENE4|EntrezGene|ID4|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP:::ID4:1 0/0:50 1/0:50 1/0:50:AD:::ID4:1 1/0:50 0/0:50 -2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP 0/0:50 1/0:50 1/0:50:AD 1/0:50 0/0:50 -3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP 0/0:50 1/0:50 1/0:50:AD 1/0:50 0/0:50 -4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 -4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID8:1 1/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 -4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 +2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:3_2_C_G 0/0:50 1/0:50 1/0:50:AD,AR_C:3_2_C_G 1/0:50 0/0:50 +3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:2_1_C_G 0/0:50 1/0:50 1/0:50:AD,AR_C:2_1_C_G 1/0:50 0/0:50 +4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123458_C_G,4_123459_C_G::ID8:1 1/0:50 0/0:50 +4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID8:1 1/0:50 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123459_C_G::ID8:1 1/0:50 0/0:50 +4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123458_C_G::ID8:1 1/0:50 0/0:50 5 123457 . C G . PASS CSQ=B|1|G|GENE1|EntrezGene|ID1a|1|AR,P|1|G|GENE2|EntrezGene|ID2a||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2a:1 0/0:50 0/0:50 1/0:50:AD_IP:::ID2a:1 0/0:50 1/0:50 -5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::::0 1/1:50 0/1:50 1/0:50:AD::::0 1/1:50 0/0:50 -6 123457 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21,ID22 2/0:50 2/0:50 1/0:50:AD_IP:::ID22:1 0/0:50 1/0:50 -6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21 2/.:50 3/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AD::::0 1/0:50 3/3:50 1/0:50:AD::::0 1/1:50 0/0:50 -6 123459 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID21,ID22:1 0/1:50 0/1:50 1/0:50:AD:::ID22 0/2:50 2/2:50 -6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T::ID21:1 1/2:50 0/3:50 2/0:50:AD::::0 2/0:50 0/0:50 -6 123461 . C G,A . PASS CSQ=P|1|G|GENE4|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP:::ID21:1 2/0:50 1/0:50 2/2:50:AR,AD:::ID21:1 1/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T::ID21:1 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T::ID21,ID22:1 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 -7 123460 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123461 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID21:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD,AR_C:5_123459_C_G::ID3a:1 1/0:50 0/0:50 +5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::::0 1/1:50 0/1:50 1/0:50:AD,AR_C:5_123458_C_G::ID3a:1 1/1:50 0/0:50 +6 123457 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22 2/0:50 2/0:50 1/0:50:AD_IP,AR_C:6_123458_C_G/A/T,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/0:50 1/0:50 +6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21 2/.:50 3/0:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21:1 1/0:50 0/0:50 +6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AD::::0 1/0:50 3/3:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A,6_123460_C_G/A/T::ID21:1 1/1:50 0/0:50 +6 123459 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP:::ID21,ID22:1 0/1:50 0/1:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/2:50 2/2:50 +6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T::ID21:1 1/2:50 0/3:50 2/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T::ID21:1 2/0:50 0/0:50 +6 123461 . C G,A . PASS CSQ=P|1|G|GENE24|EntrezGene|ID24|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP:::ID24:1 2/0:50 1/0:50 2/2:50:AR,AD:::ID24:1 1/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G::ID23:1 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G::ID23:1 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 +7 123460 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123461_C_G::ID23:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123461 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123460_C_G::ID23:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 X 123457 . C G . PASS CSQ=P|1|G|GENE5|EntrezGene|ID5||XLR,P|1|G|GENE7|EntrezGene|ID7||XLD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD:::ID7:1 0/0:50 0/0:50 1/0:50:XLD:::ID7:1 0/0:50 1/0:50 X 123458 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6|| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD ./.:50 0/0:50 1/0:50:XLD 1/0:50 0/0:50 X 123459 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6||XLR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR:::ID6:1 0/1:50 0/1:50 1/0:50:XLD::::0 1/0:50 0/0:50 diff --git a/src/test/resources/expected_noPed.vcf b/src/test/resources/expected_noPed.vcf index 465287c..b2dc020 100644 --- a/src/test/resources/expected_noPed.vcf +++ b/src/test/resources/expected_noPed.vcf @@ -41,30 +41,30 @@ ##contig= ##fileDate=20200320 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Mother Father Patient2 Mother2 Father2 -1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2:1 0/0:50 0/0:50 1/0:50:AD:::ID2:1 0/0:50 1/0:50:AD:::ID2:1 -1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD::::0 1/0:50:AD::::0 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID3:1 1/1:50:AR,AD:::ID3:1 0/1:50:AD::::0 1/0:50:AD::::0 1/1:50:AR,AD:::ID3:1 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID1,ID2:1 0/1:50:AD:::ID2:1 0/1:50:AD:::ID2:1 1/0:50:AD:::ID2:1 1/0:50:AD:::ID2:1 0/0:50 -1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 1/0:50:AD,AR_C:1_123458_C_G::ID3:1 0/0:50 1/0:50:AD::::0 1/0:50:AD::::0 0/0:50 +1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2:1 0/0:50 0/0:50 1/0:50:AD,AR_C:1_123459_C_G::ID1,ID2:1 0/0:50 1/0:50:AD:::ID2:1 +1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:1_123460_C_G::ID3:1 ./.:50 0/0:50 1/0:50:AD,AR_C:1_123459_C_G,1_123460_C_G::ID3:1 1/0:50:AD,AR_C:1_123460_C_G::ID3:1 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID3:1 1/1:50:AR,AD:::ID3:1 0/1:50:AD::::0 1/0:50:AD,AR_C:1_123458_C_G,1_123460_C_G::ID3:1 1/1:50:AR,AD:::ID3:1 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID1,ID2:1 0/1:50:AD:::ID2:1 0/1:50:AD:::ID2:1 1/0:50:AD,AR_C:1_123457_C_G::ID1,ID2:1 1/0:50:AD:::ID2:1 0/0:50 +1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:1_123458_C_G::ID3:1 1/0:50:AD,AR_C:1_123458_C_G::ID3:1 0/0:50 1/0:50:AD,AR_C:1_123458_C_G,1_123459_C_G::ID3:1 1/0:50:AD,AR_C:1_123458_C_G::ID3:1 0/0:50 1 123461 . C G . PASS CSQ=P|1|G|GENE4|EntrezGene|ID4|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID4:1 0/0:50 1/0:50:AD:::ID4:1 1/0:50:AD:::ID4:1 1/0:50:AD:::ID4:1 0/0:50 -2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD 0/0:50 1/0:50:AD 1/0:50:AD 1/0:50:AD 0/0:50 -3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD 0/0:50 1/0:50:AD 1/0:50:AD 1/0:50:AD 0/0:50 -4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50:AD:::ID8:1 0/0:50 -4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 1/0:50:AD:::ID8:1 0/0:50 1/0:50:AD:::ID8:1 1/0:50:AD:::ID8:1 0/0:50 -4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50:AD:::ID8:1 0/0:50 +2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:3_2_C_G 0/0:50 1/0:50:AD,AR_C:3_2_C_G 1/0:50:AD,AR_C:3_2_C_G 1/0:50:AD,AR_C:3_2_C_G 0/0:50 +3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:2_1_C_G 0/0:50 1/0:50:AD,AR_C:2_1_C_G 1/0:50:AD,AR_C:2_1_C_G 1/0:50:AD,AR_C:2_1_C_G 0/0:50 +4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123458_C_G,4_123459_C_G::ID8:1 1/0:50:AD,AR_C:4_123458_C_G,4_123459_C_G::ID8:1 0/0:50 +4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 1/0:50:AD:::ID8:1 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123459_C_G::ID8:1 1/0:50:AD,AR_C:4_123457_C_G,4_123459_C_G::ID8:1 0/0:50 +4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID8:1 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123458_C_G::ID8:1 1/0:50:AD,AR_C:4_123457_C_G,4_123458_C_G::ID8:1 0/0:50 5 123457 . C G . PASS CSQ=B|1|G|GENE1|EntrezGene|ID1a|1|AR,P|1|G|GENE2|EntrezGene|ID2a||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID2a:1 0/0:50 0/0:50 1/0:50:AD:::ID2a:1 0/0:50 1/0:50:AD:::ID2a:1 5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP 1/0:50 ./.:50 0/0:50 1/0:50 1/0:50 0/0:50 5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP 1/1:50 1/1:50 0/1:50 1/0:50 1/1:50 0/0:50 -6 123457 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21,ID22:1 2/0:50 2/0:50 1/0:50:AD:::ID22:1 0/0:50 1/0:50:AD:::ID22:1 -6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21:1 2/.:50 3/0:50 1/0:50:AD::::0 1/0:50:AD,AR_C:6_123459_C_G/A::ID21:1 0/0:50 -6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AR,AD,AR_C:7_123459_C_G,6_123457_C_G/A,6_123460_C_G/A/T,6_123458_C_G/A/T,7_123460_C_G::ID21:1 1/0:50:AD,AR_C:6_123460_C_G/A/T,6_123459_C_G/A,6_123458_C_G/A/T::ID21:1 3/3:50 1/0:50:AD::::0 1/1:50:AR,AD:::ID21:1 0/0:50 -6 123459 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID21,ID22:1 0/1:50:AD,AR_C:7_123459_C_G,6_123457_C_G/A,6_123460_C_G/A/T,6_123459_C_G/A/T,6_123458_C_G/A/T::ID21,ID22:1 0/1:50:AD,AR_C:6_123457_C_G/A,6_123460_C_G/A/T,7_123459_C_G,6_123458_C_G/A/T::ID21,ID22:1 1/0:50:AD:::ID22:1 0/2:50 2/2:50 -6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21:1 1/2:50:AR,AD,AR_C:7_123459_C_G,6_123457_C_G/A,6_123459_C_G/A,6_123459_C_G/A/T,6_123458_C_G/A/T::ID21:1 0/3:50 2/0:50 2/0:50 0/0:50 -6 123461 . C G,A . PASS CSQ=P|1|G|GENE4|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID21:1 2/0:50 1/0:50:AD:::ID21:1 2/2:50 1/0:50:AD:::ID21:1 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21:1 1/0:50:AD,AR_C:6_123460_C_G/A/T,6_123459_C_G/A,6_123458_C_G/A/T::ID21:1 0/0:50 0/0:50 0/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21,ID22:1 0/0:50 0/1:50:AD,AR_C:6_123457_C_G/A,6_123460_C_G/A/T,6_123459_C_G/A,6_123458_C_G/A/T::ID21,ID22:1 0/0:50 0/0:50 0/0:50 -7 123460 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123461 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID21:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +6 123457 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 2/0:50 2/0:50 1/0:50:AD,AR_C:6_123458_C_G/A/T,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/0:50 1/0:50:AD:::ID22:1 +6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21:1 2/.:50 3/0:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21:1 1/0:50:AD,AR_C:6_123459_C_G/A,6_123460_C_G/A/T::ID21:1 0/0:50 +6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AR,AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123460_C_G/A/T::ID21:1 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A,6_123460_C_G/A/T::ID21:1 3/3:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A,6_123460_C_G/A/T::ID21:1 1/1:50:AR,AD:::ID21:1 0/0:50 +6 123459 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD:::ID21,ID22:1 0/1:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/1:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/2:50 2/2:50 +6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T::ID21:1 1/2:50:AR,AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A,6_123459_C_G/A/T::ID21:1 0/3:50 2/0:50 2/0:50 0/0:50 +6 123461 . C G,A . PASS CSQ=P|1|G|GENE24|EntrezGene|ID24|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD:::ID24:1 2/0:50 1/0:50:AD:::ID24:1 2/2:50 1/0:50:AD:::ID24:1 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G::ID23:1 1/0:50:AD::::0 0/0:50 0/0:50 0/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G::ID23:1 0/0:50 0/1:50:AD::::0 0/0:50 0/0:50 0/0:50 +7 123460 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123461_C_G::ID23:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123461 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123460_C_G::ID23:1 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 X 123457 . C G . PASS CSQ=P|1|G|GENE5|EntrezGene|ID5||XLR,P|1|G|GENE7|EntrezGene|ID7||XLD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD:::ID7:1 0/0:50 0/0:50 1/0:50:XLD:::ID7:1 0/0:50 1/0:50:XLD:::ID7:1 X 123458 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6|| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD ./.:50 0/0:50 1/0:50:XLD 1/0:50:XLD 0/0:50 X 123459 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6||XLR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR:::ID6:1 0/1:50:XLD::::0 0/1:50:XLD::::0 1/0:50:XLD::::0 1/0:50:XLD::::0 0/0:50 diff --git a/src/test/resources/expected_noVEPinheritance.vcf b/src/test/resources/expected_noVEPinheritance.vcf index 8d1451e..b4020e4 100644 --- a/src/test/resources/expected_noVEPinheritance.vcf +++ b/src/test/resources/expected_noVEPinheritance.vcf @@ -39,10 +39,10 @@ ##contig= ##fileDate=20200320 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Mother Father Patient2 Mother2 Father2 -1 123457 . C G . PASS CSQ=G|GENE1|EntrezGene|ID1|,G|GENE2|EntrezGene|ID2| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1 0/0:50:AD 0/0:50:AD 1/0:50:AD_IP 0/0:50 1/0:50:AD_IP -1 123458 . C G . PASS CSQ=G|GENE3|EntrezGene|ID3| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD ./.:50:AD 0/0:50:AD 1/0:50:AD 1/0:50 0/0:50:AD -1 123459 . C G . PASS CSQ=G|GENE3|EntrezGene|ID3| GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0 1/1:50:AD_IP 0/1:50:AD_IP 1/0:50:AD 1/1:50 0/0:50:AD -1 123459 . C G . PASS CSQ=G|GENE1|EntrezGene|ID1|,G|GENE2|EntrezGene|ID2| GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0 0/1:50:AR,AD_IP 0/1:50:AR,AD_IP 1/0:50:AD 1/0:50 0/0:50:AD +1 123457 . C G . PASS CSQ=G|GENE1|EntrezGene|ID1|,G|GENE2|EntrezGene|ID2| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1 0/0:50:AD 0/0:50:AD 1/0:50:AD_IP,AR_C:1_123459_C_G::ID1,ID2 0/0:50 1/0:50:AD_IP,AR_C:1_123459_C_G::ID1,ID2 +1 123458 . C G . PASS CSQ=G|GENE3|EntrezGene|ID3| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD ./.:50:AD 0/0:50:AD 1/0:50:AD,AR_C:1_123459_C_G::ID3 1/0:50 0/0:50:AD,AR_C:1_123459_C_G::ID3 +1 123459 . C G . PASS CSQ=G|GENE3|EntrezGene|ID3| GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0 1/1:50:AD_IP 0/1:50:AD_IP 1/0:50:AD,AR_C:1_123458_C_G::ID3 1/1:50 0/0:50:AD,AR_C:1_123458_C_G::ID3 +1 123459 . C G . PASS CSQ=G|GENE1|EntrezGene|ID1|,G|GENE2|EntrezGene|ID2| GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0 0/1:50:AR,AD_IP 0/1:50:AR,AD_IP 1/0:50:AD,AR_C:1_123457_C_G::ID1,ID2 1/0:50 0/0:50:AD,AR_C:1_123457_C_G::ID1,ID2 X 123457 . C G . PASS CSQ=G|GENE4|EntrezGene|ID4|,G|GENE6|EntrezGene|ID6| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD::1 0/0:50:XLD 0/0:50:XLD 1/0:50:XLD 0/0:50 1/0:50:XLD X 123458 . C G . PASS CSQ=G|GENE5|EntrezGene|ID5| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD ./.:50:XLD 0/0:50:XLD 1/0:50:XLD 1/0:50 0/0:50:XLD X 123459 . C G . PASS CSQ=G|GENE5|EntrezGene|ID5| GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR::0 0/1:50:XLD,XLR 0/1:50:XLD,XLR 1/0:50:XLD 1/0:50 0/0:50:XLD diff --git a/src/test/resources/expected_probands.vcf b/src/test/resources/expected_probands.vcf index 16f3c49..87d06c2 100644 --- a/src/test/resources/expected_probands.vcf +++ b/src/test/resources/expected_probands.vcf @@ -41,30 +41,30 @@ ##contig= ##fileDate=20200320 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Patient Mother Father Patient2 Mother2 Father2 -1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID2 0/0:50 0/0:50 1/0:50:AD_IP:::ID2:1 0/0:50 1/0:50 -1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0::0 1/1:50 0/1:50 1/0:50:AD::::0 1/1:50 0/0:50 -1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0:ID1,ID2:1 0/1:50 0/1:50 1/0:50:AD:::ID2:1 1/0:50 0/0:50 -1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0::0 1/0:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 +1 123457 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID2 0/0:50 0/0:50 1/0:50:AD_IP,AR_C:1_123459_C_G::ID1,ID2:1 0/0:50 1/0:50 +1 123458 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:1_123460_C_G::ID3 ./.:50 0/0:50 1/0:50:AD,AR_C:1_123459_C_G,1_123460_C_G::ID3:1 1/0:50 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0::0 1/1:50 0/1:50 1/0:50:AD,AR_C:1_123458_C_G,1_123460_C_G::ID3:1 1/1:50 0/0:50 +1 123459 . C G . PASS CSQ=P|1|G|GENE1|EntrezGene|ID1|1|AR,P|1|G|GENE2|EntrezGene|ID2||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0:ID1,ID2:1 0/1:50 0/1:50 1/0:50:AD,AR_C:1_123457_C_G::ID1,ID2:1 1/0:50 0/0:50 +1 123460 . C G . PASS CSQ=P|1|G|GENE3|EntrezGene|ID3|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:1_123458_C_G:0:ID3:1 1/0:50 0/0:50 1/0:50:AD,AR_C:1_123458_C_G,1_123459_C_G::ID3:1 1/0:50 0/0:50 1 123461 . C G . PASS CSQ=P|1|G|GENE4|EntrezGene|ID4|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0:ID4:1 0/0:50 1/0:50 1/0:50:AD:::ID4:1 1/0:50 0/0:50 -2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0 0/0:50 1/0:50 1/0:50:AD 1/0:50 0/0:50 -3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0 0/0:50 1/0:50 1/0:50:AD 1/0:50 0/0:50 -4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID8 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 -4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::1:ID8:1 1/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 -4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD::1:ID8 0/0:50 0/0:50 1/0:50:AD:::ID8:1 1/0:50 0/0:50 +2 1 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:3_2_C_G:0 0/0:50 1/0:50 1/0:50:AD,AR_C:3_2_C_G 1/0:50 0/0:50 +3 2 empty_gene C G . PASS CSQ=P|1|G|UNUSED_GENE_NAME|||| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:2_1_C_G:0 0/0:50 1/0:50 1/0:50:AD,AR_C:2_1_C_G 1/0:50 0/0:50 +4 123457 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID8 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123458_C_G,4_123459_C_G::ID8:1 1/0:50 0/0:50 +4 123458 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::1:ID8:1 1/0:50 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123459_C_G::ID8:1 1/0:50 0/0:50 +4 123459 . C G . PASS CSQ=P|1|G|GENE8|EntrezGene|ID8||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD::1:ID8 0/0:50 0/0:50 1/0:50:AD,AR_C:4_123457_C_G,4_123458_C_G::ID8:1 1/0:50 0/0:50 5 123457 . C G . PASS CSQ=B|1|G|GENE1|EntrezGene|ID1a|1|AR,P|1|G|GENE2|EntrezGene|ID2a||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID2a 0/0:50 0/0:50 1/0:50:AD_IP:::ID2a:1 0/0:50 1/0:50 -5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0::0 1/1:50 0/1:50 1/0:50:AD::::0 1/1:50 0/0:50 -6 123457 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T:1:ID21,ID22 2/0:50 2/0:50 1/0:50:AD_IP:::ID22:1 0/0:50 1/0:50 -6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T::ID21 2/.:50 3/0:50 1/0:50:AD::::0 1/0:50 0/0:50 -6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AD::0::0 1/0:50 3/3:50 1/0:50:AD::::0 1/1:50 0/0:50 -6 123459 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0:ID21,ID22:1 0/1:50 0/1:50 1/0:50:AD:::ID22 0/2:50 2/2:50 -6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T:0:ID21:1 1/2:50 0/3:50 2/0:50 2/0:50 0/0:50 -6 123461 . C G,A . PASS CSQ=P|1|G|GENE4|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0:ID21:1 2/0:50 1/0:50 2/2:50 1/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T:0:ID21:1 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123459_C_G/A/T:0:ID21,ID22:1 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 -7 123460 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123459_C_G/A/T:1:ID21 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123461 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::1:ID21 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD::::0 ./.:50 0/0:50 1/0:50:AD,AR_C:5_123459_C_G::ID3a:1 1/0:50 0/0:50 +5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AD_IP::0::0 1/1:50 0/1:50 1/0:50:AD,AR_C:5_123458_C_G::ID3a:1 1/1:50 0/0:50 +6 123457 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T:1:ID21,ID22 2/0:50 2/0:50 1/0:50:AD_IP,AR_C:6_123458_C_G/A/T,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/0:50 1/0:50 +6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21 2/.:50 3/0:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123459_C_G/A,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21:1 1/0:50 0/0:50 +6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/3:50:AD::0::0 1/0:50 3/3:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A,6_123460_C_G/A/T::ID21:1 1/1:50 0/0:50 +6 123459 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:AR,AD_IP::0:ID21,ID22:1 0/1:50 0/1:50 1/0:50:AD,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T,6_123460_C_G/A/T::ID21,ID22:1 0/2:50 2/2:50 +6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:6_123457_C_G/A,6_123458_C_G/A/T,6_123459_C_G/A/T:0:ID21:1 1/2:50 0/3:50 2/0:50 2/0:50 0/0:50 +6 123461 . C G,A . PASS CSQ=P|1|G|GENE24|EntrezGene|ID24|1|AD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP::0:ID24:1 2/0:50 1/0:50 2/2:50 1/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G:0:ID23:1 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD_IP,AR_C:7_123459_C_G,7_123460_C_G,7_123461_C_G:0:ID23:1 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 +7 123460 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123461_C_G:1:ID23 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123461 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:AD,AR_C:7_123459_C_G,7_123460_C_G:1:ID23 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 X 123457 . C G . PASS CSQ=P|1|G|GENE5|EntrezGene|ID5||XLR,P|1|G|GENE7|EntrezGene|ID7||XLD GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD::1:ID7 0/0:50 0/0:50 1/0:50:XLD:::ID7:1 0/0:50 1/0:50 X 123458 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6|| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD ./.:50 0/0:50 1/0:50:XLD 1/0:50 0/0:50 X 123459 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6||XLR GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR::0:ID6 0/1:50 0/1:50 1/0:50:XLD::::0 1/0:50 0/0:50 diff --git a/src/test/resources/integration.vcf b/src/test/resources/integration.vcf index 659730b..e3d23d2 100644 --- a/src/test/resources/integration.vcf +++ b/src/test/resources/integration.vcf @@ -50,16 +50,16 @@ 5 123457 . C G . PASS CSQ=B|1|G|GENE1|EntrezGene|ID1a|1|AR,P|1|G|GENE2|EntrezGene|ID2a||AD GT:DP 1/0:50 0/0:50 0/0:50 1/0:50 0/0:50 1/0:50 5 123458 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP 1/0:50 ./.:50 0/0:50 1/0:50 1/0:50 0/0:50 5 123459 . C G . PASS CSQ=B|1|G|GENE3|EntrezGene|ID3a|1|AR GT:DP 1/1:50 1/1:50 0/1:50 1/0:50 1/1:50 0/0:50 -6 123457 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP 1/0:50 2/0:50 2/0:50 1/0:50 0/0:50 1/0:50 -6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP 1/0:50 2/.:50 3/0:50 1/0:50 1/0:50 0/0:50 -6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP 1/3:50 1/0:50 3/3:50 1/0:50 1/1:50 0/0:50 -6 123459 . C G,A . PASS CSQ=P|1|G|GENE1|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP 1/1:50 0/1:50 0/1:50 1/0:50 0/2:50 2/2:50 -6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE3|EntrezGene|ID21|1|AR GT:DP 1/0:50 1/2:50 0/3:50 2/0:50 2/0:50 0/0:50 -6 123461 . C G,A . PASS CSQ=P|1|G|GENE4|EntrezGene|ID21|1|AD GT:DP 1/0:50 2/0:50 1/0:50 2/2:50 1/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP 1/0:50 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123459 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP 1/0:50 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 -7 123460 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AR GT:DP 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 -7 123461 . C G . PASS CSQ=P|1|G|GENE13|EntrezGene|ID21|1|AD GT:DP 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +6 123457 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP 1/0:50 2/0:50 2/0:50 1/0:50 0/0:50 1/0:50 +6 123458 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP 1/0:50 2/.:50 3/0:50 1/0:50 1/0:50 0/0:50 +6 123459 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP 1/3:50 1/0:50 3/3:50 1/0:50 1/1:50 0/0:50 +6 123459 . C G,A . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR,P|1|G|GENE2|EntrezGene|ID22||AD GT:DP 1/1:50 0/1:50 0/1:50 1/0:50 0/2:50 2/2:50 +6 123460 . C G,A,T . PASS CSQ=P|1|G|GENE21|EntrezGene|ID21|1|AR GT:DP 1/0:50 1/2:50 0/3:50 2/0:50 2/0:50 0/0:50 +6 123461 . C G,A . PASS CSQ=P|1|G|GENE24|EntrezGene|ID24|1|AD GT:DP 1/0:50 2/0:50 1/0:50 2/2:50 1/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP 1/0:50 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123459 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP 1/0:50 0/0:50 0/1:50 0/0:50 0/0:50 0/0:50 +7 123460 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 +7 123461 . C G . PASS CSQ=P|1|G|GENE23|EntrezGene|ID23|1|AR GT:DP 1/0:50 0/0:50 0/0:50 0/0:50 0/0:50 0/0:50 X 123457 . C G . PASS CSQ=P|1|G|GENE5|EntrezGene|ID5||XLR,P|1|G|GENE7|EntrezGene|ID7||XLD GT:DP 1/0:50 0/0:50 0/0:50 1/0:50 0/0:50 1/0:50 X 123458 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6|| GT:DP 1/0:50 ./.:50 0/0:50 1/0:50 1/0:50 0/0:50 X 123459 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID6||XLR GT:DP 1/1:50 0/1:50 0/1:50 1/0:50 1/0:50 0/0:50