how to attach XM tag - Githubissues

lh3 / bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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how to attach XM tag #352

Closed S-111 closed 2 years ago

S-111 commented 2 years ago

I would like to use XM tag after mapping, but the output sam file did not has XM tag. how to attach XM tag? I executed the command below. Thank you for your cooperation!

bwa mem -x pacbio ref.fasta input.fastq > out.sam Version: 0.7.17-r1198-dirty

lh3 commented 2 years ago

You can compute from NM and CIGAR. Also, for pacbio data, use minimap2.