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| #! /usr/bin/env python2 | |
| # $1 gene list | |
| # $2 HPO term list | |
| import urllib3 | |
| import requests | |
| import json | |
| import sys | |
| import os |
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| 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 \ |