Is there any way to do a vg mapping comparison:
Two vg gam files:
1. one from the flat graph constructed from a ref genome only
2. another graph constructed from a ref genome and variants
after mapping, the same set of reads were mapped to either graph with "vg map", I would like to see how much the read mapping was improved, e.g. total mapped reads , mapping quality through the whole graph
In addition, it is also interesting to see how well the accuracy of variants call in both vcf outputs from "vg call" for the above mentioned two vg graph. The Toil-vg has a function for accuracy evaluation but is very old. I don't know the old Toil-vg is still work or not to compare the variant accuracy.
It seems vg pack has some function, but no this summary