how to keep Mm tags in bam

[bakeronit]

Hi all,

I extracted fastq(samtools fastq -T 1) from unmapped bam to align to the genome with winnowmap. However, it lost extra tags like qs and Mm after mapping. Is there a way to keep them in the results? Or to tag them again.

Thank you. Jia

[bakeronit]

just realised that the winnowmap works like minimap2, so add -y will copy the comment info from fastq header.