Mark Fleharty
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Latest activity by Mark Fleharty-
Mark Fleharty commented,
You can still create a PoN with tumor samples, but you run the risk of constructing a PoN that will filter common driver events in your panel.
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Mark Fleharty commented,
I agree, it seems the white paper. needs to be updated. I've created a github ticket at: https://github.com/broadinstitute/gatk/issues/6965 Please feel free to add to it if I didn't capture everyt...
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Mark Fleharty commented,
If your data is on Google Cloud, that is probably easiest. Just give me permissions to access, and let me know the gs:// URL. Otherwise, dropbox, and other sharing services work.
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Mark Fleharty commented,
Yes, PBMCs are good for constructing PoNs.
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Mark Fleharty commented,
I would also encourage you to take a look at: https://www.biorxiv.org/content/10.1101/825042v1.full This describes. LinSeq, which is one of the ways we use to construct somatic truth data.
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Mark Fleharty commented,
Having 50% of indels be false positives is definitely a problem. FFPE can cause problems, but typically don't cause mapping artifacts. I would expect that mapping artifacts would be filtered well ...
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Mark Fleharty commented,
We typically used pooled Hapmap samples. We pool them in equal fractions of 5, 10 and 20 samples. This gives us a distribution of truth variants as low as 2.5% allele fraction.
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Mark Fleharty commented,
Ian Yi-Feng Chang This is a perfectly sensible step-by-step guide to use. We also provide a Terra workspace that should be more convenient to use. https://app.terra.bio/#workspaces/help-gatk/Somat...
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Mark Fleharty commented,
The whitepaper is the most up to date documentation on the theory used for M2. We have not made significant changes to the theory behind M2 in the last 10 months. Could you be more specific about ...
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Mark Fleharty commented,
The sensitivity and false positive rate you get with Mutect2 will depend on a lot of variables. How deep is your sequencing, are you doing WGS or a panel? Are your samples FFPE? Are you using a t...