From 876791f858596d005019513a563b245f16789b56 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Sat, 20 Oct 2018 18:27:31 -0700 Subject: [PATCH] Add the PS FORMAT VCF standard header field --- src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java b/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java index de2817c96b..035cdd3c39 100644 --- a/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java +++ b/src/main/java/htsjdk/variant/vcf/VCFStandardHeaderLines.java @@ -158,6 +158,7 @@ private static void registerStandard(final VCFFormatHeaderLine line) { registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification")); registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_ALLELE_DEPTHS, VCFHeaderLineCount.R, VCFHeaderLineType.Integer, "Allelic depths for the ref and alt alleles in the order listed")); registerStandard(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_FILTER_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype-level filter")); + registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_SET_KEY, 1, VCFHeaderLineType.Integer, "Phasing set (typically the position of the first variant in the set)")); registerStandard(new VCFFormatHeaderLine(VCFConstants.PHASE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Read-backed phasing quality")); // INFO lines