Brian Haas
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Recent activity by Brian Haas Sort by recent activity-
I suspect the read filters are intended to be consistent, and if there are differences it was likely an oversight. Mark Fleharty is the authority here and might comment further.
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Hi, Good question. If you're using whole exome data and have an intervals file, I think you should use that for the -L parameter, but use the common variants vcf for the -V option. If you're doing...
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Yes, I believe that should be added. The official PoN workflow commands are here:https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/mutect2_pon.wdl I'll put in a request tha...
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Hi, Can you please elaborate with some specifics? I can see that resource files listed for some parameter values are vague and don't match what's in the resource bundle. I'll look into getting t...
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Hi, The process for creating your own PoN is: To make your own PoN: You will need at least 40 normals to pass into the initial step, but the command structure for all three steps is given below....
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Also, can you please confirm that the panel of normals is excluding variants based on chromosome position and not requiring allele-specific matching? ie. a G->A variant in the tumor sample may ...
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Can I please confirm that this is the logic being used in the current PoN creation step: ==== Any candidate PoN site must occur in at least 2 samples (as per the default for --min-sample-count). If...