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This question was brought by my colleague who pursued the GATK called variants downstream. She used a program called ANNOVAR to annotate the variants derived form GATK calls from our exome-seq data. After that she saw many of variants are annotated to be at 5' or 3' UTR regions, intronic regions, or even intergenic regions. However, when I called the variants with GATK, I did use -L option at the Unified genotyper step with the bed file directly download from Agilent (I used the enrichment kit from Agilent), which supposed to restrict the variants only to the exons or exon-approximate regions. UTRs or intronic regions may be understandable, but the variants from intergenic regions are kind of odd, is it? Anybody has similar observation or just something wrong with ANNOVAR or our local setting of ANNOVAR? I hope GATK did not introduce these odds but faithfully call variants only at the target interval regions as defined to do. Unless the Agilent's target enrichment regions are spread out into intergenic regions?
Any comments or insights are appreciated!