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GATK command for adding known vcf file for SNP's so as to filter it out
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.
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