Step 3 -- incorporating SVs into patient table
The third step takes all the SV variants from all samples within each patient and present them in the same format as SNVs and incorporate SVs in the patient level table.
Default options can be found here
SV_incorporation.R doesOnly SVs implicating any ACCESS SV calling key genes are retained
Process DMP SVs to similar format to ACCESS SV output
Row-bind plasma and DMP SVs and make call level info (similar to SNVs)
Annotate call status for each call of each sample
Not Called
Not Covered -- none of the genes in key genes
Called
Read in SNV table, row-bind with SV table, write out table