From 6df113a4f92c446d70a7e580ec6b37ac1bf2f93d Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Mon, 24 Aug 2020 10:30:57 +0100
Subject: [PATCH] Helper script for gnomAD ggd recipe

---
 bcbio_gnomad_install.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100755 bcbio_gnomad_install.sh

diff --git a/bcbio_gnomad_install.sh b/bcbio_gnomad_install.sh
new file mode 100755
index 0000000..13563b6
--- /dev/null
+++ b/bcbio_gnomad_install.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#PBS -l walltime=96:00:00
+#PBS -l ncpus=1,mem=128gb
+#PBS -q uv2000
+#PBS -N bcbio_gnomad_install
+#PBS -j oe
+
+cd /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/txtmp
+
+PATH=$PATH:/home/u035/project/software/bcbio/anaconda/bin
+
+ref=../seq/hg38.fa
+fields_to_keep="INFO/"$(cat gnomad_fields_to_keep.txt | paste -s | sed s/"\t"/",INFO\/"/g)
+
+bcftools view -f PASS gnomad.genomes.r3.0.sites.vcf.bgz | bcftools annotate -x "^$fields_to_keep" -Ov | vt decompose -s - | vt normalize -r $ref -n - | vt uniq - | bgzip -c > variation/gnomad_genome.vcf.gz
+
+tabix -f -p vcf variation/gnomad_genome.vcf.gz
+tabix -f -p vcf --csi variation/gnomad_genome.vcf.gz
+
-- 
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