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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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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.
Hope to hear soon.