how does samtools mpileup handle the md tag

[Jetse]

Hello everyone,

How does samtool mpileup handle the md tag?
I want to know this because the samtools calmd program takes over the 8 hours too execute on a single bam file, and my bam files become larger because of the extra tag. So does samtools calmd increase the accuracy or sensitivity of a multi sampled samtools mpileup?

[lh3]

It does not look at the MD tag.

[Jetse]

Thanks!
I have found some additional information about this subject at the samtools website:

The BAQ strategy is invoked by default in mpileup. To make other SNP callers take advantage of BAQ, one should run

samtools calmd -Abr aln.bam ref.fa > aln.baq.bam

to cap base quality by BAQ and then give aln.baq.bam to the SNP callers as the input. For high-coverage single-sample SNP calling, BAQ appears to be as effective as multi-sequence realignment, while being much faster and easier to use. Currently the BAQ strategy is the only practical way to avoid the INDEL artifact in low-coverage multi-sample SNP calling.