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Kate Megquier

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Latest activity by Kate Megquier
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    Kate Megquier commented,

    Hello, I was wondering whether there are any updates on the Mutect2 pipeline for liquid biopsy? Best, Kate

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    Kate Megquier commented,

    Thank you so much, Genevieve! I was only able to post a few of our plots here, would it be possible for me to share the remaining plots with you directly to get your opinion on them?

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    Kate Megquier created a post,

    AnalyzeCovaiates BQSR plots on canine data

    Dear GATK team, We ran BQSR on canine cancer (60x) and germline (30x) WGS samples on Terra, using a modified version of the showcase preprocessing WDL (removing the alignment step, as the bams had ...

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    Kate Megquier commented,

    Dear Bhanu Gandham, Thank you for your reply! Yes, we have read through the tutorial docs and found them very helpful, but were still unsure of why a CNV might be called significant in one sample a...

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    Kate Megquier created a post,

    CNV not called in some samples

    Dear GATK Team,   We've noticed a CNV being called in some samples, but not being called as significant in others, despite a mean log2 copy ratio of -26, and are unsure why this is happening.   We ...

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    Kate Megquier commented,

    Dear Andrey, Thank you very much for your reply! Increasing the  `-number-of-changepoints-penalty-factor` to 5 seems to smooth things out quite a bit.  In terms of enabling GC correction, I don't s...

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    Kate Megquier created a post,

    Smoothing noisy tumor-only CNV data?

    Hello, We ran the GATK somatic CNV calling pipeline on Terra (v1.3.1 for the PoN and 1.3.0 for the somatic pair workflow) on unpaired canine tumor WGS data.  Our CNV plots are very noisy. See below...

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    Kate Megquier created a post,

    Allelic fraction NaNs in CNV pipeline

    Dear GATK Team, I had previously asked the following question: I ran the GATK somatic CNV calling pipeline on Terra (v1.3.1 for the PoN and 1.3.0 for the somatic pair workflow) on unpaired canine t...