Program to calculate and add the NM tag to a bam file

Question

[abascalfederico]

Does anybody know of a program to add the NM tag (number of mismatches) to a BAM file?

Usually aligned BAM files come with that tag, but I've found one without it and need that information.

Thanks!

[pammybiotech]

Hello

I've created an alignment (SAM and subsequently BAM file) using samtools. However, when I'm trying to create an index out of the BAM file I get the following message:

[E::hts_idx_push] Region 536876664..536876746 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6

I have no clue what that means so any help would be much appreciated

Thanks

Answer 1

[trausch]

samtools calmd <aln.bam> <ref.fasta>

[abascalfederico]

That's exactly what I needed, thanks!