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Does providing an exome target interval list overlook many non-targeted, high-quality SNPs?
Hi GATK Team,
I recently came across a paper that states that exome sequencing can generate high-quality SNPs in non-targeted regions, and even in regions far from the targets: ncbi.nlm.nih.gov/pubmed/22607156. I just completed variant calling on some exome data and used the kit manufacturer's exome target list to restrict the variant calling during the process. However, I wonder if, in retrospect, this was the best thing to do.
I will likely go back and redo the variant calling without an exome target interval list to see how many other SNPs (if any) we get but I just wanted to post this reference here in case other GATK users (particularly those doing exome sequencing) find it interesting and perhaps ask the GATK team if they had any thoughts on not using exome interval lists during variant calling on exome data? Perhaps it's just a tradeoff between time and overall SNP count...
Anyway, thank you and keep up the good work.