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Merge pull request #99 from molgenis/fix/sample_csq_filtering
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Fix: sample classification mismatching CSQ order and size
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@dennishendriksen
dennishendriksen authored Nov 21, 2024
2 parents c1379cf + 9096f50 commit d2ec47c
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Showing 5 changed files with 18 additions and 19 deletions.
21 changes: 10 additions & 11 deletions src/main/java/org/molgenis/vcf/decisiontree/filter/SampleClassifierImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ private VcfRecord processRecordSample(
for (SampleContext sampleContext : samplesContexts) {
if (sampleContext.getProband()) {
List<Decision> sampleDecisions = new ArrayList<>();
processRecord(vcfRecord, decisionTree, vcfMetadata, nestedHeaderLine, alleleCsqMap,
processRecord(vcfRecord, decisionTree, vcfMetadata, alleleCsqMap,
sampleContext, sampleDecisions);
sampleAnnotator.annotate(sampleDecisions, sampleContext.getIndex(), vcBuilder);
decisions.addAll(
Expand All @@ -87,22 +87,21 @@ private VcfRecord processRecordSample(

private void processRecord
(VcfRecord vcfRecord, DecisionTree decisionTree, VcfMetadata vcfMetadata,
NestedHeaderLine nestedHeaderLine, Map<Integer, List<VcfRecord>> alleleCsqMap,
Map<Integer, List<VcfRecord>> alleleCsqMap,
SampleContext sampleContext,
List<Decision> sampleDecisions) {
for (int alleleIndex = 0; alleleIndex < vcfRecord.getNrAltAlleles(); alleleIndex++) {
Integer vepAlleleIndex = alleleIndex + 1;
Allele allele = vcfRecord.getAltAllele(alleleIndex);
List<VcfRecord> singleCsqRecords = alleleCsqMap.get(vepAlleleIndex);
if (singleCsqRecords == null || singleCsqRecords.isEmpty()) {
singleCsqRecords = List.of(
vepHelper.createEmptyCsqRecord(vcfRecord, vepAlleleIndex, nestedHeaderLine));
}
for (VcfRecord singleCsqRecord : singleCsqRecords) {
Variant variant = Variant.builder().vcfMetadata(vcfMetadata).vcfRecord(singleCsqRecord)
.allele(allele).build();
sampleDecisions.add(
decisionTreeExecutor.execute(decisionTree, variant, sampleContext));
//only classify samples if a CSQ is present
if(singleCsqRecords != null) {
for (VcfRecord singleCsqRecord : singleCsqRecords) {
Variant variant = Variant.builder().vcfMetadata(vcfMetadata).vcfRecord(singleCsqRecord)
.allele(allele).build();
sampleDecisions.add(
decisionTreeExecutor.execute(decisionTree, variant, sampleContext));
}
}
}
}
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4 changes: 2 additions & 2 deletions src/test/resources/example_samples-classified-noPPP.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -84,5 +84,5 @@
1 16375586 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false:AR_C ./.:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375587 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1/1:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false:AR_C .|.:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375588 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false:AR_C 1:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375589 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375590 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375589 . A C,G . PASS CSQ=G|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|,C|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false,class_false:,:family&proband_hom_ref&depth&read_depth&alleles&exit_false,family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50:.:.:.:.:.:class_false,class_false:,:family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false,family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false 0|0:50,0:50:.:.:.:.:.:class_false,class_false:,:family&proband_hom_ref&depth&read_depth&alleles&exit_false,family&proband_hom_ref&depth&read_depth&alleles&exit_false
1 16375590 . G A,T . PASS CSQ=T|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_false 0|0:50,0:50:.:.:.:.:.:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false
4 changes: 2 additions & 2 deletions src/test/resources/example_samples-classified.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -82,5 +82,5 @@
1 16375586 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 1/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true:AR_C ./.:25,25:50 0|0:50,0:50
1 16375587 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 1/1:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true:AR_C .|.:25,25:50 0|0:50,0:50
1 16375588 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true:AR_C 1:25,25:50 0|0:50,0:50
1 16375589 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375590 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375589 . A C,G . PASS CSQ=G|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|,C|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false,class_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375590 . G A,T . PASS CSQ=T|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false:AR_C 1:25,25:50 0|0:50,0:50
4 changes: 2 additions & 2 deletions src/test/resources/example_samples-classified_paths-labels.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -84,5 +84,5 @@
1 16375586 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_true:AR_C ./.:25,25:50 0|0:50,0:50
1 16375587 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1/1:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_true:AR_C .|.:25,25:50 0|0:50,0:50
1 16375588 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_true GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 1|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_true::family&proband_hom_ref&depth&read_depth&alleles&genotype&phenotype&exit_true:AR_C 1:25,25:50 0|0:50,0:50
1 16375589 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375590 . GA G . PASS CSQ=-|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375589 . A C,G . PASS CSQ=G|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|,C|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0/0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false,class_false:,:family&proband_hom_ref&depth&read_depth&alleles&exit_false,family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50 0|0:50,0:50
1 16375590 . G A,T . PASS CSQ=T|intron_variant|MODIFIER|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||7/19|NM_000085.5:c.656-31del|||||||rs751608665|1||1||1|EntrezGene||||||||uncertain_significance&pathogenic||1||||||||20|45|-14|-45|0.05|0.00|0.00|0.00|CLCNKB|VUS|0.032507|HP:0000951||AR|LP||||1:16375584-16375585|0.000548455|0|638508|Conflicting_interpretations_of_pathogenicity||criteria_provided&_conflicting_interpretations|LP|filter&vkgl&exit_lp|;VIPC_S=class_false GT:AD:DP:VI:VIC:VID:VIG:VIM:VIPC_S:VIPL_S:VIPP_S:VIS 0|0:25,25:50:AR:1_16376412_G_A,1_16376412_G_N:0:1188:1:class_false::family&proband_hom_ref&depth&read_depth&alleles&exit_false:AR_C 1:25,25:50 0|0:50,0:50
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