new (experimental) option -n added to vg deconstruct. Like -a, it genotypes nested sites, but unlike -a it does so top-down, setting various tags that keep track of the nesting relationship at the allele level (and also linking every site back to its position on the LV=0 reference chromosome). *-alleles (used in recent VCF versions to represent spanning alleles) are used. This option will not support nested insertions on GBZ/GBWT input -- so in practice it should be used on chromosome-level .vg files (I will look into relaxing this).
Changelog Entry
To be copied to the draft changelog by merger:
-nadded tovg deconstruct. Like-a, it genotypes nested sites, but unlike-ait does so top-down, setting various tags that keep track of the nesting relationship at the allele level (and also linking every site back to its position on the LV=0 reference chromosome). *-alleles (used in recent VCF versions to represent spanning alleles) are used. This option will not support nested insertions on GBZ/GBWT input -- so in practice it should be used on chromosome-level.vgfiles (I will look into relaxing this).Description