Added description of the gtcCallRate field in the VCF Header. (#1730)

broadinstitute · Oct 12, 2021 · b5732e1 · b5732e1
1 parent 43a962e
commit b5732e1
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diff --git a/src/main/java/picard/arrays/GtcToVcf.java b/src/main/java/picard/arrays/GtcToVcf.java
@@ -209,6 +209,8 @@ protected int doWork() {
             // The Call Rate in the Illumina GTC File does not take into account zeroed out SNPs.
             // So we recalculate it (and ignore zeroed out assays - which also includes intensity only probes)
             vcfHeader.addMetaDataLine(new VCFHeaderLine(InfiniumVcfFields.GTC_CALL_RATE, String.valueOf(callRate)));
+            vcfHeader.addMetaDataLine(new VCFHeaderLine(InfiniumVcfFields.GTC_CALL_RATE_DETAIL,
+                    "The gtcCallRate is the Call Rate reported in the Illumina GTC file, corrected for the presence of Zeroed-Out SNPs"));
 
             writeVcf(contexts, OUTPUT, refSeq.getSequenceDictionary(), vcfHeader);
 

diff --git a/src/main/java/picard/arrays/illumina/InfiniumVcfFields.java b/src/main/java/picard/arrays/illumina/InfiniumVcfFields.java
@@ -46,6 +46,7 @@ public class InfiniumVcfFields {
     public static final String EXPECTED_GENDER = "expectedGender";
     public static final String FINGERPRINT_GENDER = "fingerprintGender";
     public static final String GTC_CALL_RATE = "gtcCallRate";
+    public static final String GTC_CALL_RATE_DETAIL = "gtcCallRateDetail";
     public static final String AUTOCALL_GENDER = "autocallGender";
     public static final String AUTOCALL_DATE = "autocallDate";
     public static final String IMAGING_DATE = "imagingDate";