update CreateSomaticPanelOfNormals javadoc #6584
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| @@ -31,8 +31,7 @@ | |||
| * | |||
| * <p> | |||
| * The tool takes multiple normal sample callsets produced by {@link Mutect2}'s tumor-only mode and collates sites present in two or more samples | |||
| * into a sites-only VCF. The PoN captures common artifactual and germline variant sites. | |||
| * Mutect2 then uses the PoN to filter variants at the site-level. | |||
| * into a sites-only VCF. The PoN captures common artifacts. Mutect2 then uses the PoN to filter variants at the site-level. | |||
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thanks for the update! Can I suggest being explicit about specifically not intending to capture germline variants? I'm pretty sure that the code and default settings indicate that if the probability(germline) > 0.5 then it's excluded from the PoN. This probability is configurable by CLI parameter. Similarly, the number of samples required is configurable by a CLI parameter. I only discovered this after digging deeply, as it's not advertised well elsewhere.
fleharty
approved these changes
May 7, 2020
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Looks good to me. I think @brianjohnhaas makes a good point too.
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@fleharty This will be quick.