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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
• September 07, 2021 15:31
• 2 followers
• 3 comments
• 0 votes

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
• August 05, 2021 18:17
• 6 followers
• 13 comments
• 0 votes

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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
• July 14, 2021 17:30
• 5 followers
• 4 comments
• 0 votes

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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
• April 01, 2021 15:23
• 2 followers
• 1 comment
• 1 vote

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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
• January 26, 2021 17:42
• 6 followers
• 10 comments
• 0 votes

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
• May 18, 2020 17:50
• 2 followers
• 3 comments
• 0 votes