From e5998be0a9a3b566ef90e8742225ec4f404bed17 Mon Sep 17 00:00:00 2001 From: David Benjamin Date: Fri, 29 Oct 2021 13:38:41 -0400 Subject: [PATCH] genotype-germline-sites not called experimental --- .../hellbender/tools/walkers/mutect/M2ArgumentCollection.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java index bc22c13e7ee..924061a9630 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java @@ -124,10 +124,10 @@ public ReadThreadingAssembler createReadThreadingAssembler(){ public boolean genotypePonSites = false; /** - * Usually we exclude sites in the panel of normals from active region determination, which saves time. Setting this to true + * Usually we exclude germline sites from active region determination to save runtime. Setting this to true * causes Mutect to produce a variant call at these sites. This call will still be filtered, but it shows up in the vcf. */ - @Argument(fullName= GENOTYPE_GERMLINE_SITES_LONG_NAME, doc="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered.", optional = true) + @Argument(fullName= GENOTYPE_GERMLINE_SITES_LONG_NAME, doc="Call all apparent germline site even though they will ultimately be filtered.", optional = true) public boolean genotypeGermlineSites = false; /**