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Different number of rejected variants detected when scanning whole genome and intervals.
I ran MuTect using a tumor-normal pair to detect variants from whole genome, and I got 'N' number of rejected variants (R).
Then, I reran MuTect using the same tumor-normal pair but on selected intervals defined as follow: one base pair before and after the positions of the rejected variants (R).
I thought that the same number of rejected variants (N) will be returned, but the number of rejected variants (based on intervals) increases. Intervals are saved in .bed
Did I do something wrong? Thanks!
p/s: I would like to know the reasons of variants being rejected, but the first iteration was run without enabling the extended output flag. So, to save time, i chose to rerun MuTect only on the sites where rejected variants are detected.