Padding of exonic intervals
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2.2 years ago
NGSCanBioinf ▴ 10

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.

next-gen • 753 views
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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.

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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.

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