I used GATK 3.3 for calling SNPs for my exome data. I also restricted my SNPs to be called specifying a BED file. When I annotated the vcf file i get lot of SNPs as intronic. What can be its possible reason?
So, did you check where the variants are located and whether they are really outside your targets?
This can depend on how your target intervals are designed, whether you used padding or not, and other factors. Did you check where those intronic SNPs are located and how their location relates to the target intervals?
Well I provided the Bed file as an interval list, of the exome capture kit. And there are chances that because of that there might be presence of some amount of intronic SNPs occurrence. But the amount is quite high in comparison to the exonic ones. Even if the padding is kept 25 bps for exons does that makes so much of difference while calling?
We used Nextera rapid exome capture kit and it is mentioned at the Illumina site that they have targeted only exonic regions!! So there was no padding used while designing!