pbmm2 no NM tag? - Githubissues

KolmogorovLab / Severus

A tool for somatic structural variant calling using long reads

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pbmm2 no NM tag? #6

Closed jo-mc closed 1 year ago

jo-mc commented 1 year ago

Just running a test and noticed error with pbmm2 no NM tag. Looked at a few other of my pbmm2 files and none seem to have NM?. These are from a few years ago. Its running ok with minimap bams.

mikolmogorov commented 1 year ago

Maybe an older version of pbmm? I believe the most recent versions should have it. Could you send output of samtools view pbmm.bam -H | grep PG?

jo-mc commented 1 year ago

Sure: @PG ID:pbmm2 PN:pbmm2 VN:1.4.0 (commit 1.4.0) CL:pbmm2 align /ref/chm13/chm13.draft_v1.0.fasta googson.fofn HG.bam --preset CCS --sort -j 20 -J 4 --rg @RG\tID:HG\tSM:chm13.HG --unmapped @PG ID:samtools PN:samtools PP:pbmm2 VN:1.17 CL:samtools view -H HG.bam

OK, I see it was added in pbmm2 1.10:

1.10.0:
- Allow reverse-complemented unaligned records as input
- Allow infix, but not flanking, spaces in sample name
- Do not allow overwriting input files
- Store number of mismatches, tag NM