vg: transfer FASTQ comment to SAM tag a la `bwa mem -C`

Question

[tahermun]

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 SAM tag format in our fastq file that we want to transfer over to the BAM output in VG.

If not already implemented, could I request this as a feature?

Answer 1

[Jordan M Eizenga]

This feature has been added and should be included in the next scheduled release. The option is called --comments-as-tags, and it's available in all of vg's mapping tools.