Converting gam to gaf

Question

[hmg]

I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert gam to gaf? Gaf is definitely easier to parse than using jq for the json conversion of gam, but I'd like to avoid realigning all my previous work. Are there plans to make a gaf output option for vg view?

Answer 1

[glenn.hickey]

GAF will gradually be more tightly integrated with all the tools. In the meantime, you can convert back and forth between GAM and GAF with vg convert -F and -G

[colindaven]

For future reference - the command for this in vg convert is somewhat unclear - you need to have a vg format graph in the command, that is, you cannot just directly convert gam to gaf or vice versa.

vg convert --threads $task.cpus $vg --gam-to-gaf $gam > ${prefix}.gaf