Skip to content

Commit

Permalink
Merge pull request #65 from molgenis/fix/missingValues
Browse files Browse the repository at this point in the history 
Use dot for missing values as required by the VCF spec
  • Loading branch information
@dennishendriksen
dennishendriksen authored Dec 10, 2024
2 parents ae10576 + 902c864 commit d4dd968
Show file tree
Hide file tree
Showing 5 changed files with 89 additions and 93 deletions.
14 changes: 5 additions & 9 deletions src/main/java/org/molgenis/vcf/inheritance/matcher/Annotator.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,7 @@
import static org.molgenis.vcf.utils.utils.HeaderUtils.fixVcfInfoHeaderLines;

import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFFormatHeaderLine;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.*;

import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -71,7 +67,7 @@ private htsjdk.variant.variantcontext.Genotype annotateGenotype(InheritanceResul
GenotypeBuilder genotypeBuilder = new GenotypeBuilder(genotype);
Set<String> vig = new HashSet<>();
Set<String> compounds = getCompoundStrings(inheritanceResult.getCompounds());
String vic = inheritanceResult.getCompounds().isEmpty() ? "" : String.join(",", compounds.stream().sorted().toList());
String vic = inheritanceResult.getCompounds().isEmpty() ? VCFConstants.MISSING_VALUE_v4 : String.join(",", compounds.stream().sorted().toList());
MatchEnum match = getMatch(inheritanceResult, vcfRecord);
Set<String> vi = mapInheritanceModes(inheritanceResult);
String vim = mapInheritanceMatch(match);
Expand All @@ -82,7 +78,7 @@ private htsjdk.variant.variantcontext.Genotype annotateGenotype(InheritanceResul
genotypeBuilder.attribute(INHERITANCE_MODES, String.join(",", vi));
genotypeBuilder.attribute(INHERITANCE_MATCH, vim);
genotypeBuilder.attribute(POSSIBLE_COMPOUND, vic);
genotypeBuilder.attribute(MATCHING_GENES, vig.stream().sorted().collect(Collectors.joining(",")));
genotypeBuilder.attribute(MATCHING_GENES, vig.isEmpty() ? VCFConstants.MISSING_VALUE_v4 : vig.stream().sorted().collect(Collectors.joining(",")));
genotypeBuilder.attribute(DENOVO, mapDenovoValue(inheritanceResult, sample));
return genotypeBuilder.make();
}
Expand Down Expand Up @@ -111,7 +107,7 @@ private static String mapDenovoValue(InheritanceResult inheritanceResult, Sample
return switch (inheritanceResult.getDenovo().get(sample)) {
case TRUE -> "1";
case FALSE -> "0";
case POTENTIAL -> "";
case POTENTIAL -> VCFConstants.MISSING_VALUE_v4;
};
}

Expand All @@ -120,7 +116,7 @@ private static String mapInheritanceMatch(MatchEnum match) {
switch (match) {
case TRUE -> inheritanceMatch = "1";
case FALSE -> inheritanceMatch = "0";
case POTENTIAL -> inheritanceMatch = "";
case POTENTIAL -> inheritanceMatch = VCFConstants.MISSING_VALUE_v4;
default -> throw new UnexpectedEnumException(match);
}
return inheritanceMatch;
Expand Down
56 changes: 28 additions & 28 deletions src/test/resources/expected_noParents.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,36 +41,36 @@
##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,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
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,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,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
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,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
X 123460 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID13||XL GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD:::ID13:1 0/1:50 0/1:50 1/1:50:XLD,XLR:::ID13:1 1/0:50 0/0:50
X 123461 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID13||XL GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR:::ID13:1 0/1:50 0/1:50 1/0:50:XLD:::ID13:1 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
X 123460 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID13||XL GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:XLD:.:.:ID13:1 0/1:50 0/1:50 1/1:50:XLD,XLR:.:.:ID13:1 1/0:50 0/0:50
X 123461 . C G . PASS CSQ=P|1|G|GENE6|EntrezGene|ID13||XL GT:DP:VI:VIC:VID:VIG:VIM 1/1:50:XLD,XLR:.:.:ID13:1 0/1:50 0/1:50 1/0:50:XLD:.:.:ID13:1 1/0:50 0/0:50
Y 123457 . C G . PASS CSQ=P|1|G|GENE9|EntrezGene|ID9|| GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:YL ./.:50 0/0:50 1/0:50:YL ./.:50 0/0:50
Y 123458 . C G . PASS CSQ=P|1|G|GENE10|EntrezGene|ID10||YL GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:YL:::ID10 ./.:50 0/0:50 1/0:50:YL:::ID10 ./.:50 0/0:50
Y 123459 . C G . PASS CSQ=P|1|G|GENE11|EntrezGene|ID11||YL GT:DP:VI:VIC:VID:VIG:VIM 1:50:YL:::ID11:1 .:50 0:50 1:50:YL:::ID11:1 .:50 0:50
Y 123458 . C G . PASS CSQ=P|1|G|GENE10|EntrezGene|ID10||YL GT:DP:VI:VIC:VID:VIG:VIM 1/0:50:YL:.:.:ID10 ./.:50 0/0:50 1/0:50:YL:.:.:ID10 ./.:50 0/0:50
Y 123459 . C G . PASS CSQ=P|1|G|GENE11|EntrezGene|ID11||YL GT:DP:VI:VIC:VID:VIG:VIM 1:50:YL:.:.:ID11:1 .:50 0:50 1:50:YL:.:.:ID11:1 .:50 0:50
MT 123459 . C G . PASS CSQ=P|1|G|GENE12|EntrezGene|ID12|| GT:DP:VI:VIC:VID:VIG:VIM 1:50:MT .:50 0:50 1:50:MT .:50 0:50
Loading

0 comments on commit d4dd968

Please sign in to comment.