Regarding parameters in angsd -baq:1 and :baq:2

Question

[a4appy23]

Im trying to find heterozygosity using angsd software. So while dealing with the parameter , baq: (base alignment quality) to correct the misalignments i was wondering what is the difference between setting baq: 1(normal baq) and baq:2 (extended baq)?

Answer 1

[alexjvr]

Basically BAQ 2 should discover more SNPs but at the cost of accuracy (i.e. more false positives) compared to BAQ 1. ANGSD suggests that there is no best BAQ, but that it depends on the data.

There's a useful discussion on the ANGSD user forum here and here