Hi,
I want to add a known vcf file of snps maybe from one of the databases of snp and want to remove those snp's if they also occur in my sample. How can I do this in GATK.
Also I am interested in A-->G mutations, but on the reverse strand this would be a T-->C mutation which I would like to capture of course. How can I get to know the strand specificity.
Hope to hear soon.
Regards
Varun