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,