Scripts and example data for generating refGene and PolyPhen2 annotations for variants using ANNOVAR.Recommend using full path to input data for each script. ANNOVAR documentation: http://annovar.openbioinformatics.org/en/latest/
Run table_annovar.pl on multiple VCFs on Blue Waters, generating refGene and PolyPhen2 annotations. Modify variables internally.
Options:
QUEUE=normal
email=
nodes=1
thr=32
pbswalltime=00:20:00
QSUB_HEAD="#!/bin/bash"
SUFFIX=vcf
JOB_DIR=/full/path/to/job_dir
OUT_DIR=/full/path/to/output_dir
ANNOVAR_DIR=/full/path/to/annovar