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Qing Zhang

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  • Total activity 21
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Activity overview

Latest activity by Qing Zhang
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    Qing Zhang commented,

    1. Community
    2. General Discussion
    3. somatic CNV pipeline segmentation with custom het list?

    Thanks Pamela. After some discussion with Sam on slack, I think we are going to do this by replacing "allelic-counts" with custom hets genotypes by ourselves, set all filtering criteria to be as le...

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    Qing Zhang created a post,

    somatic CNV pipeline segmentation with custom het list?

    1. Community
    2. General Discussion

    Hi, I want to get allelic copy ratio for each segment with my customized hets list (we have a slightly different way to define "heterozygous in normal" from GATK's), like Allelic Capseg does. It se...

    • Qing Zhang
    • 2 followers
    • 3 comments
    • 0 votes
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    Qing Zhang commented,

    1. Community
    2. General Discussion
    3. somatic CNV PoN recommendation?

    Hi, I want hg38 CNV PoN, not SNV. Is there a public CNV PoN for somatic analysis?

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    Qing Zhang created a post,

    somatic CNV PoN recommendation?

    Answered
    1. Community
    2. General Discussion

    is there a recommended source of somatic CNV PoN that works with the latest GATK? (I know I can build my own, but just wonder if one from a larger cohort already exists)

    • Qing Zhang
    • 6 followers
    • 13 comments
    • 0 votes
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    Qing Zhang created a post,

    GATK funcotator transcript selection criteria

    Answered
    1. Community
    2. General Discussion

    Hi, We used Funcotator to annotate somatic calls and were confused about the transcript selection mode, the default "canonical" mode sometimes chooses a different transcript than what is better kno...

    • Qing Zhang
    • 5 followers
    • 4 comments
    • 0 votes
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    Qing Zhang created a post,

    funcotator annotation for non-left-aligned indels

    1. Community
    2. General Discussion

    For non-left aligned indels, funcotator is able to annotate the correct functional changes but there are minor differences in cDNA between left-aligned indel vs non-left-aligned ones. The correspon...

    • Qing Zhang
    • 2 followers
    • 1 comment
    • 1 vote
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    Qing Zhang commented,

    1. Community
    2. Somatic
    3. No headers found in VCF

    Sorry I found the problem! I was not populating the headers correctly - I missed `##` in some lines. Thanks!

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    Qing Zhang created a post,

    No headers found in VCF

    1. Community
    2. Somatic

    Hi GATK Team, I am working on a pipeline that has to write a minimal VCF to be funcotated. However, when I run `Funcotator` or `ValidateVariants`, I got the following error: ``` htsjdk.tribble.Trib...

    • Qing Zhang
    • 6 followers
    • 10 comments
    • 0 votes
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    Qing Zhang commented,

    1. Community
    2. Somatic
    3. mutect2 realignment

    Thanks, David, this is very helpful.   Just to double-check, if I did not run M2 with --debug, there is no way that I can retrieve those realigned intervals?   Thanks!

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    Qing Zhang created a post,

    mutect2 realignment

    1. Community
    2. Somatic

    Hi GATK Team, I wonder if there is any indication in the outputs / intermediate files for regions that triggered M2 realignment if I did not use -bamout in M2?  My another question is, what should ...

    • Qing Zhang
    • 2 followers
    • 3 comments
    • 0 votes