mvelinder

set -oexu pipefail

VCF=$1

bcftools csq \
	-f /scratch/ucgd/lustre/work/u0691312/reference/ucgd_reference/GRCh38/human_g1k_v38_decoy_phix.fasta \
	-g /scratch/ucgd/lustre/work/u0691312/reference/Homo_sapiens.GRCh38.100.gff3.gz \
	$VCF \
	| vcfanno -p 12 \
	/scratch/ucgd/lustre/work/u0691312/reference/vcfanno_revel.toml \

mvelinder

#! /usr/bin/env python2

# $1 gene list
# $2 HPO term list

import urllib3
import requests
import json
import sys
import os