Fixed Number entry of CNLP field in gCNV intervals VCF.

broadinstitute · Mar 21, 2019 · 93f4022 · 93f4022
1 parent 5149c18
commit 93f4022
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/...g/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java b/...g/broadinstitute/hellbender/tools/copynumber/gcnv/GermlineCNVIntervalVariantComposer.java
@@ -78,7 +78,7 @@ public void composeVariantContextHeader(final Set<VCFHeaderLine> vcfDefaultToolH
                 VCFHeaderLineType.Integer, "Genotype"));
         result.addMetaDataLine(new VCFFormatHeaderLine(CN, 1,
                 VCFHeaderLineType.Integer, "Copy number maximum a posteriori value"));
-        result.addMetaDataLine(new VCFFormatHeaderLine(CNLP, VCFHeaderLineCount.A,
+        result.addMetaDataLine(new VCFFormatHeaderLine(CNLP, VCFHeaderLineCount.UNBOUNDED,
                 VCFHeaderLineType.Integer, "Copy number log posterior (in Phred-scale) rounded down"));
         result.addMetaDataLine(new VCFFormatHeaderLine(CNQ, 1,
                 VCFHeaderLineType.Integer, "Genotype call quality as the difference between" +

diff --git a/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_000.vcf b/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_000.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number maximum a posteriori value">
-##FORMAT=<ID=CNLP,Number=A,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
+##FORMAT=<ID=CNLP,Number=.,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
 ##FORMAT=<ID=CNQ,Number=1,Type=Integer,Description="Genotype call quality as the difference between the best and second best phred-scaled log posterior scores">
 ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">

diff --git a/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_001.vcf b/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_001.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number maximum a posteriori value">
-##FORMAT=<ID=CNLP,Number=A,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
+##FORMAT=<ID=CNLP,Number=.,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
 ##FORMAT=<ID=CNQ,Number=1,Type=Integer,Description="Genotype call quality as the difference between the best and second best phred-scaled log posterior scores">
 ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">

diff --git a/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_002.vcf b/...oadinstitute/hellbender/tools/copynumber/gcnv-postprocess/intervals_output_SAMPLE_002.vcf
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number maximum a posteriori value">
-##FORMAT=<ID=CNLP,Number=A,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
+##FORMAT=<ID=CNLP,Number=.,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
 ##FORMAT=<ID=CNQ,Number=1,Type=Integer,Description="Genotype call quality as the difference between the best and second best phred-scaled log posterior scores">
 ##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">