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='mkdir -p log; snakemake -p --ri --jobname "{rulename}.{jobid}" --drmaa " -P eichlerlab -q eichler-short.q -l h_rt=48:00:00 -l mfree={resources.mem}G -pe serial {threads} -R y -V -cwd -S /bin/bash " --drmaa-log-dir $PWD/log --latency-wait 60'

Genotype

snakesub -j [max_jobs] get_tables

Plot

snakesub -j [max_jobs]