I'm running Freebayes as follows:
freebayes -f genome.fa --pooled-discrete --genotype-qualities --read-mismatch-limit 70 \ tumour.bam normal.bam -v tn_raw.vcf
I want to filter out reads that are soft clipped (aligned with bwa mem) > 70 bps, and I'm using the
--read-mismatch-limit 70 option to achieve this. However, in the output I see SNPS being called from reads with > 80 bps mis-aligned (see linked screenshot):
Is this option doing what I think it is? Is this the correct option to exclude reads with more than N mismatches?