Question: How to get the simple somatic mutation vcf file from GDC data portal?
2
gravatar for Vasu
17 months ago by
Vasu340
Vasu340 wrote:

Hi,

I wanted to download WXS somatic mutation file (VCF format) from GDC data portal vcf file in gdc portal. With the vcf file I would like to do the Snpeff annotation.

How to get all the samples mutational data in a single vcf file?

In an other way I tried getting the mutational data from xena browser which is a txt file. But the file is not working for Snpeff annotation. Snpeff needs a vcf file for annotation. Is there a way to convert a normal txt or csv file into vcf?

I also tried getting mutational data using "TCGAbiolinks" R package TCGAbiolinks mutational data. From this I'm able to get only "maf" file. Is there a way to convert maf file to vcf format so that it can be used for Snpeff annotation.

Any help would be appreciated.

mutations gdc tcgabiolinks maf vcf • 1.3k views
ADD COMMENTlink written 17 months ago by Vasu340

For mutation data in the TCGA, only the MAF files are open access. If you want to obtain the VCF files, you will have to request the controlled / restricted access to the TCGA.

ADD REPLYlink written 17 months ago by Kevin Blighe45k

Yes, Thank you. What if I download the maf files using "TCGAbiolinks" and Is there a way to convert maf file to vcf format?

ADD REPLYlink written 17 months ago by Vasu340

Yes, please refer to Cyriac at MSKCC: Tool or Script to convert MAF file to VCF ?

ADD REPLYlink written 17 months ago by Kevin Blighe45k

Thank you. BTW from "Xena browser" I got the tsv file mutational data tsv file. Any idea how to convert tsv to vcf?

ADD REPLYlink written 17 months ago by Vasu340
1

Without looking, I imagine that this TSV file is similar to the MAF format, with a few columns removed, possibly. The MAF format is a tab-separated file.

I would recommend you to download the MAF file from the GDC and then try to convert to VCF with Cyriac's function

ADD REPLYlink written 17 months ago by Kevin Blighe45k
1

Sure. Thank you very much !!

ADD REPLYlink written 17 months ago by Vasu340
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