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.