vg call is time consuming

Question

[Maxine]

The vg call command, which follows vg augment, is as follows:

vg call ${aug_xg} -k ${aug_pack} -r ${aug_snarls} -t 30 -a -A > ${aug_vcf}

It has been running for 30 hours and has only produced an empty ${aug_vcf} file so far. This is likely due to the large size of the graph. The input sizes are:

• ${aug_xg}: 117G
• ${aug_pack}: 4.7G
• ${aug_snarls}: 1.1G

Is there anything I can do to expedite the vg call process? For instance, would vg chunk it by chromosome help? I would appreciate any advice.

Thanks,
Maxine

Answer 1

[glenn.hickey]

The next vg release will have a patch to vg call

https://github.com/vgteam/vg/pull/4252

that fixes up the -C (maximum allele cutoff) to be more robust, which should in turn allow calling any graph in reasonable time. It also adds a (fairly basic) --progress option that may give you a better sense of what the tool is doing when.

[Maxine]

Those fixes are really helpful. Thanks for notice!