Open alshai opened 1 month ago
We don't have this at the moment. We might be able to turn FASTQ comments into one of our internal annotations and then represent them in SAM output, but we'd have to pull the flag for this down into the general readers and writers somehow.
I'd recommend doing something like:
join
to graft the FASTQ comments onto the ends of the corresponding SAM lines.But that's definitely way more passes than just bringing the information through during mapping.
Is there anything similar in VG to the -C option in BWA MEM?
From the BWA mem manual
Basically we have a comment in our FASTQ that is formatted like a SAM tag that we want to transfer over to the BAM output in VG.
If not already implemented, could I request this as a feature?