Any option like BWA MEM '-C'?

[alshai]

Is there anything similar in VG to the -C option in BWA MEM?

From the BWA mem manual

-C Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.

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?

[adamnovak]

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:

• Pull out all the FASTQ header lines and sort by read name
• Get all the SAM lines and sort by read name
• Use Unix 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.