Question: Program to calculate and add the NM tag to a bam file
0
gravatar for abascalfederico
2.3 years ago by
abascalfederico1.1k
Spain
abascalfederico1.1k wrote:

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 • 1.5k views
ADD COMMENTlink modified 11 months ago by pammybiotech0 • written 2.3 years ago by abascalfederico1.1k
3
gravatar for trausch
2.3 years ago by
trausch1.4k
Germany
trausch1.4k wrote:

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

ADD COMMENTlink written 2.3 years ago by trausch1.4k

That's exactly what I needed, thanks!

ADD REPLYlink written 2.3 years ago by abascalfederico1.1k
0
gravatar for pammybiotech
11 months ago by
pammybiotech0 wrote:

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

ADD COMMENTlink written 11 months ago by pammybiotech0
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