Andrey Smirnov
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Activity overview
Latest activity by Andrey Smirnov-
Andrey Smirnov commented,
Hi Xscrapert, I apologize for the late response. It looks like in your DetermineContigPloidy command you set path to /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359...
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Andrey Smirnov commented,
Joshua Davies we do not have a standard tool for performing CNV validation. CNV pipeline (https://github.com/broadinstitute/gatk/tree/master/scripts/cnv_wdl/germline) has few QC steps that will mar...
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Andrey Smirnov commented,
Hi yang S, you can find a common site file you can use here gs://gatk-test-data/cnv/somatic/somatic-hg38_af-only-gnomad.hg38.AFgt0.02.interval_list. You can also find instructions on how to generat...
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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.