This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Program to calculate and add the NM tag to a bam file

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!

bam nm
• 6,858 views • link
updated by Biostar Biostar • written by abascalfederico abascalfederico

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

• 0 views • link
updated by Ram Ram • written by pammybiotech • pammybiotech

1 answer

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

• 0 views • link
written by trausch trausch

Log in to answer this question.

More posts like this