Andrey Smirnov
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Activity overview
Latest activity by Andrey Smirnov-
Andrey Smirnov commented,
SkyWarrior You can use PreprocessIntervals GATK tool perform interval padding for you. Also see the full recommended gCNV workflow here: https://github.com/broadinstitute/gatk/blob/master/scripts/c...
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Andrey Smirnov commented,
Official comment Hi SkyWarrior, Computation of the copy ratios is done prior to running segmentation step in the post processing. 'Copy ratios' are a function of some posterior values and so it is normal to see sig...
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Andrey Smirnov commented,
Hi Yizhou Wang, If your samples are all normal I would suggest using the Germline CNV (gCNV) workflow. Four, however, is very few samples to do analysis with. Do you have more normal mice samples ...
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Andrey Smirnov commented,
Official comment Bilyana Stoilova, Thank you for your kind words about our tools. I can try to answer your questions. 1. You can definitely use `--neutral-segment-copy-ratio-upper-bound` and `--neutral-segment-copy...
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Andrey Smirnov commented,
Sergey Naumenko, `CreateReadCountPanelOfNormals` has multiple arguments for filtering input count matrix, such as `--minimum-interval-median-percentile`, `--maximum-zeros-in-sample-percentage` etc ...
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Andrey Smirnov commented,
Hi Kate Pal, I was a little confused by your post. I am assuming the problem is with CreateReadCountPanelOfNormals tool, not DetermineGermlineContigPloidy? If so, it looks like the exception that c...
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Andrey Smirnov commented,
Sophie Agger I'm one of the developers of GATK gCNV. We have always used BAMs that are preprocessed using GATK best practices for running GATK gCNV, so I would recommend doing that.
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Andrey Smirnov commented,
Vishal Mishra You cannot analyze a single exome with GATK gCNV. For running GATK Germline CNV pipeline you will need to first learn a gCNV "ploidy model" and "denoising model" using a cohort of sa...
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Andrey Smirnov commented,
Hi Kate Megquier There is no explicit option in the Somatic Pair Workflow. The GC correction will be performed automatically if the panel of normals was created with a GC annotated interval list (i...
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Andrey Smirnov commented,
Hi SkyWarrior, The differences in the new release are explained in this pull request that is part of 4.1.4.1 now - https://github.com/broadinstitute/gatk/pull/6245 The error that you got was due to...