read_depth_genotyper

Get genotypes for regions using WSSD and SUNK

Install

git clone --recursive https://github.com/EichlerLab/read_depth_genotyper.git

alias snakesub_sge='mkdir -p log; snakemake --ri -k --jobname "{rulename}.{jobid}" --drmaa " -V -cwd -j y -o ./log -e ./log {params.sge_opts} -w n -S /bin/bash" -w 60'

Genotype

snakesub_sge -j [max_jobs] -T get_tables

Plot

snakesub_sge -T -j [max_jobs]