Hi @fulvio.dan,
I hope all is well! I had a question about the variant files here (syn8466424). I am trying to figure out what each column header is. My best guess, looking at syn8466471 as an example is the following:
"Pos", "Name", "Chr", "Start", "End", "Ref", "Alt", Unknown, Unknown, Unknown, Unknown
Apologies if this is some standard format, but as far as I could tell this is not a standard VCF or MAF.
Thanks!
Robert
Created by Robert Allaway allawayr Thank you Fulvio, this is very helpful! I appreciate it!
Cheers,
Robert Hi Robert,
You are right, the variants files I uploaded are not in VCF or MAF standard formats. They are the output of GATK HaplotypeCaller annotated by AnnoVar.
The column headers are
Column #1: "Func.refGene" (AnnVar)
Column #2: "Gene.refGene" (AnnVar)
Column #3: "Chr" (GATK HaplotypeCaller)
Column #4: "Start" (GATK HaplotypeCaller)
Column #5: "End" (GATK HaplotypeCaller)
Column #6: "Ref" (GATK HaplotypeCaller)
Column #7: "Alt" (GATK HaplotypeCaller)
Column #8: "Genotype" (GATK HaplotypeCaller)
Column #9: "Qual" (GATK HaplotypeCaller)
Column #10: "Genotype Quality" (GATK HaplotypeCaller)
Thank you.
Best,
Fulvio
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