Hi,

I have one .vcf file of whole genome sequencing of tumour Vs normal samples of 21 patients.

I need a data from like this as input for a tool for finding driver genes 

 

    > head(mutations)
      sampleID chr      pos ref mut
    1 Sample_1   1   871244   G   C
    2 Sample_1   1  6648841   C   G
    3 Sample_1   1 17557072   G   A
    4 Sample_1   1 22838492   G   C
    5 Sample_1   1 27097733   G   A
    6 Sample_1   1 27333206   G   A

In separated .vcf files for each patient I have start, end, chromosome, ref, and variant allele. However I am sure how to get such data frame from this big vcf

Any help please?

Thank you

Using *bcftools*:

    bcftools query -f '[%SAMPLE %CHROM %POS %REF %ALT %GT\n]' myFile.vcf > myFileLong.txt