Consider removing the BAQ option in samtools mpileup

[mfoll]

Adding the --no-BAQ in samtools mpileup causes:

Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.

Disabling the BAQ makes it roughly 33% faster, so we should evaluate if this is necessary in the case of needlestack (in particular when we do ABRA).