The genome graph is created from multiple genome alignment with 'vg construct', e.g. from 4 genomes, named: A, B, C, D
Now we want to call variants with ‘vg call’ from packed graph alignment file (.pack). Command:
vg call -t 10 graph.vg -k graph.pack -a >graph.gam.vcf
[This will use default for all paths since without giving customized '–p' ]
We then checked the number of variants called relative to all paths. I pasted the summary below. The first column is the path name or genome name. The second column is the number of variants.
- Question one
It seems like these represent variants calls such that the variant will only be called relative to D if it is in a highly nested variant (I.e. Variant within a variant within a variant etc). Is this interpretation correct?
- Question two
It seems that the default order of variant calls, when variant-nesting occurs, are in alphabetic order of paths. How can we get the variants for paths in a supplied order, e.g. in the order of C, B, A, D, instead of A, B, C, D? I know I can specify a subset of individual paths with -p, but these are still ordered and reported alphabetically.