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genotype-germline-sites not called experimental #7533

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Oct 31, 2021
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genotype-germline-sites not called experimental #7533

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4 changes: 2 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
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Expand Up @@ -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;

/**
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