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Qing Zhang

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  • somatic CNV pipeline segmentation with custom het list?

    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...

  • somatic CNV PoN recommendation?

    Answered

    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)

  • GATK funcotator transcript selection criteria

    Answered

    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...

  • funcotator annotation for non-left-aligned indels

    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...

  • No headers found in VCF

    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...

  • mutect2 realignment

    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 ...