How to get the simple somatic mutation vcf file from GDC data portal?

Question

[Vasu]

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.

[Kevin Blighe]

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.

[Vasu]

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

[Kevin Blighe]

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

[Vasu]

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

[Kevin Blighe]

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

[Vasu]

Sure. Thank you very much !!