DELISHUS: Deletion Inference from SNP Data


java -Xmx[size] -jar delishus.jar [parameters]
where [size] is the size of Java's heap. This must be large enough to store the input genotype matrix and underlying graph structures.
Required parameters
-p [pfile]
sets the input PED file to be [pfile]. Note that the allele designation is different from standard map files. View DELISHUS Input and Output for more details.
-m [mfile]
sets the input MAP file to be [mfile]
-t [threshold]
use [threshold] as the minimum clique size to call a deletion. For modern GWAS data [threshold]=5 is sensitive enough to compute small deletions while keeping false positives low.
-o [dir]
output results to directory [dir]
-c [chr]
process chromosome [chr] of the input MAP/PED files

This material is based upon work supported by the National Science Foundation under Grant Number 1048831. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.