vg sort gam file by read name

Question

[Yihang]

I wonder if there is a way to sort gam file via vg by the read names. I know there is a command vg gamsort but it seems that this tool does not sort the gam file by name.

Thanks!

Answer 1

[glenn.hickey]

There is no command to do it directly. You can convert to GAF and sort that though:

vg convert graph.vg -G aln.gam | sort -k1 | vg convert graph.vg -F - > aln.sorted.gam