I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN.
VARSCAN takes an input in pileup format.
I could get the pileup files for all 100 SRAs using NCBI SRA Tools. But not able to give the List of pileup files to Varscan, in order to generate VCF files.
Is there a way I could generate VCF files from all 100 pileup files at one go or a way to generate VCF files directly from NCBI SRA ?
any advice and suggestions will be appreciated..