stoat change‐ref - Pa-Tou/stoat GitHub Wiki

This is a post-processing step to switch the output of stoat to a new reference. Note that this is not equivalent to running the pipeline with a different reference. Since the variant calls are relative to one reference, off-reference calls may be different.

stoat change-ref takes as input the TSV output of stoat (stoat.assoc.pvalues.tsv), a graph, a distance index, and a list of new references. The new references must be the names of paths in the graph, which can be found by running

vg paths -L -x [graph] > [reference names]

The command can be run as:

stoat change-ref -T [stoat.assoc.pvalues.tsv] -g [graph] -d [distance-index] -r [reference names] > [renamed_tsv]