Dear Fritz,
I tried to filter out SVs occurring in assembly gaps, represented in bed format, using SURVIVOR filter. I noticed that some SVs partially overlapping a gap were not filtered out, while using bedtools intersect with default parameters (namely 1bp overlap is enough to have a match) they were. Are only SVs fully overlapping a region in the bed filtered out by SURVIVOR? Is there any threshold set? Thanks in advance.
Simone
Dear Fritz, I tried to filter out SVs occurring in assembly gaps, represented in bed format, using
SURVIVOR filter. I noticed that some SVs partially overlapping a gap were not filtered out, while usingbedtools intersectwith default parameters (namely 1bp overlap is enough to have a match) they were. Are only SVs fully overlapping a region in the bed filtered out by SURVIVOR? Is there any threshold set? Thanks in advance. Simone