David Benjamin
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Activity overview
Latest activity by David Benjamin-
David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
yb87625 This looks like a possible bug. Could you share your pileups.table input file?
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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
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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David Benjamin commented,
You would get three numbers for MMQ if there are two alt alleles. Why are you generating GVCF files?
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David Benjamin commented,
Yes, just a lot of .dot files.
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David Benjamin commented,
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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David Benjamin commented,
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...