exome sequence analysis
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7.0 years ago

In VCf file, format GT:AD:GP and its value in tumor and normal column I found no values.

I got vcf from maf2vcf script.

so is there any issue in my vcf files?

link for my vcf file https://drive.google.com/file/d/0B7mEab-MoAOueUR2NlgwX0RGSm8/view?usp=sharing

 

exome vcf • 1.5k views
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7.0 years ago

That's fine. MAF files simply don't hold that information, so place-holder values are used instead.

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Hi ryan

while I convert my maf file in to vcf I got some warning like these...

WARNING: Skipping variant at 4:100265826. Failed to fetch bps from reference FASTA!
WARNING: Skipping variant at 2:89082219. Failed to fetch bps from reference FASTA!
WARNING: Skipping variant at 2:89083945. Failed to fetch bps from reference FASTA!

and  when I go through some vcf files example there they show the DP values

what I am asking is...Is my vcf file which I give you link above is correct?

 

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Yes, as I wrote above, the file you posted is fine. You'll want to sort it though (vcftools has a vcf-sort command).

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