Pindel considers reads or fragments?

[anjulka]

I'm trying to decide how to best set my filters for Pindel. While my insert size is ~150 in a number of samples, we're sequencing 2x100bp, which means that the reads do overlap regularly. MuTect only counts one read in these circumstances. As far as I can tell from reading, it looks like Pindel would doublecount indels in the overlapping regions. Is that correct or does Pindel also only count one read from overlapping regions?

Thanks.