I'm planning to generate a
mpileup file for SNP calling. When I look for examples online I notice many turn off samtools' base alignment quality (BAQ) setting by specifying
samtools -B -f ref.fa data.bam > out.mpileup
Are samtools BAQ and GATK's IndelRealigner analogous commands for dealing with indels? Is it safe to turn off BAQ after IndelRealignment?