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Add and fix tests
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@bartcharbon
bartcharbon committed Dec 6, 2024
1 parent 3ac0ac2 commit f207aec
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Showing 6 changed files with 82 additions and 79 deletions.
5 changes: 4 additions & 1 deletion src/test/resources/ArCompoundTests.tsv
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Expand Up @@ -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
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
44 changes: 22 additions & 22 deletions src/test/resources/expected_noParents.vcf
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Expand Up @@ -41,30 +41,30 @@
##contig=<ID=MT,length=16569,assembly=b37>
##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
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40 changes: 20 additions & 20 deletions src/test/resources/expected_noPed.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -41,30 +41,30 @@
##contig=<ID=MT,length=16569,assembly=b37>
##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
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