Hi all!
After moving from bwa version 0.5.8c to 0.7.10 I discovered differences that look like errors in the newer version: it seems as BWA doesn't perform soft-clipping anymore, resulting in false positive variant calls:
Is that true? I could find parameters to disable soft-clipping, but no parameter to explicitly turn on soft-clipping.
Both version were used with default parameters (both, "bwa aln" and "bwa sampe").
Any help would be appreciated!
Thank you in advance,
Sebastian
After moving from bwa version 0.5.8c to 0.7.10 I discovered differences that look like errors in the newer version: it seems as BWA doesn't perform soft-clipping anymore, resulting in false positive variant calls:
Is that true? I could find parameters to disable soft-clipping, but no parameter to explicitly turn on soft-clipping.
Both version were used with default parameters (both, "bwa aln" and "bwa sampe").
Any help would be appreciated!
Thank you in advance,
Sebastian
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