exome sequence analysis

Question

[ashishchahl]

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

Answer 1

[Devon Ryan]

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

[ashishchahl]

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?

[Devon Ryan]

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