Padding of exonic intervals
Hello, I am running WES samples through gatk based NGS pipeline. I have a BED file limited to exonic intervals. When I use this BED file the variant calling is limited to exonic intervals which saves time but I am concerned that some splicing variants may be excluded. One solution would be to padd the intervals by say 10bp on each side, but I assume this would negatively affect the coverage analysis of the intervals as to my knowledge the coverage is calculated as the average of the provided intervals. Thanks for your feedback.
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Coverage is the absolute number of reads spanning a given genomic position, that is unaffected by any interval decision. I think you don't have to worry here. It is actually common to extend the boundaries a bit to cover the splice junctions.
Thank you for your reply. I have seen both per base coverage output which makes a very long file and also per interval coverage output, I was referring to the latter in this case.