Qing Zhang
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Recent activity by Qing Zhang Sort by recent activity-
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...
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somatic CNV PoN recommendation?
Answeredis 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)
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GATK funcotator transcript selection criteria
AnsweredHi, 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...
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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...
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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...
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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 ...