medgenru

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medgenru
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Russia
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  • > @bhanuGandham said: > Hi @medgenru > > Can you please post: > 1. the version of GATK used > 2. the exact commands for CNNScoreVariants and FilterVariantTranches > 3. entire error log Sorry for late response. Problem …
  • Okay, so i reread thru best practices and experimented a bit, and now i have question regarding HC and CNN. Do i have to run HaplotypeCaller in AS GVCF mode or nonAS standard VCF to smoothely run annotation proccess in CNN and FilterVariantTranches…
  • > @bhanuGandham said: > Hi @medgenru > > Take a look at my previous post. > What is this resource vcf you are using --resource 00-All.vcf.gz? You should use a list of validated VCFs with known sites of common variation as a resou…
  • Hello, i have same error and i cant figure out what is the problem. I've built pipeline from gatk best practices for germline snp+indels for single-sample data, all steps work fine up until filtering tranches. Command that i use gatk FilterVa…