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genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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Large TDs spanning the window size lose supporting reads

RobinVanSchendel opened this issue · comments

commented

When I run Pindel on a windowsize of 1 -w 1 and I have TDs in my background, TDs that overlap a window get very little supporting reads. For example:

TD 613012 NT 0 "" ChrID 2 BP 17952802 18565815

run on window size 5:
genotypeX 29 19 8 8 16 13

but on window size 1:
genotypeX -1 18 8 8 6

is this expected behaviour and should I not use a smaller window size?