David Benjamin
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This davidben fellow's advice is solid* but you might need to scale up some values for multi-sample mode. The stride can stay at 20 but the reads per alignment start pertain to the total depth ove...
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This parameter is a performance optimization in the active region code. It is not an argument of FilterMutectCalls. It is possible that a different site near this one will be considered active an...
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yb87625 This looks like a possible bug. Could you share your pileups.table input file?
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1. The details may be found in the "Finding Active Regions" section of our documentation here: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf. Basically, there is a princ...
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Safina Most of the time this behavior is correct and becomes apparent in the bam-out file. Could you view that in IGV and post a screenshot?
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Mariana E. M. The panels of normals I generated myself using BAM files sequenced at the Broad Institute. There's no official license other than my word that anyone can use them freely. Our versio...
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You would get three numbers for MMQ if there are two alt alleles. Why are you generating GVCF files?
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Yes, just a lot of .dot files.
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Viral variant calling could, possibly, be an exceptional circumstance. I'm not sure what argument you are referring to in FilterMutectCalls, but I believe that the VariantFiltration command would ...
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We do not recommend hard filtering by AF and AD. We recommend using the defaults for Mutect2 and FilterMutectCalls except in exceptional circumstances.The argument works as intended but the intent...