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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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Pindel understimates AF

erfan1985 opened this issue · comments

commented

I have tried pindel on several exome files with known indels. Pindel can detect all but the estimated allele fraction is way bellow what it should be. In most cases where I know the indel is fully heterozygous and the AF should be around 0.5, the estimates by pindel is less than 0.2. I m now wondering what cut-off i should use for AF to call a variant. Is there a way to fix the issue? I m using the default parameters.

Thanks