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* Delete seqc2_testdata_aceseq directory * ACE-seq test dataset * testdataset additions * get beagle ref automatically * annotations testdata * testdata * small changes * beagle ref hg37 added to igenomes * testdata is running hg19
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assets/hg19/hg19_GRch37_100genomes_gc_content_10kb.txt
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set -euo pipefail | ||
# Copyright (c) 2017 The ACEseq workflow developers. | ||
# Distributed under the MIT License (license terms are at https://www.github.com/eilslabs/ACEseqWorkflow/LICENSE.txt). | ||
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usage() { echo "Usage: $0 [-r ref -m memory]" 1>&2; exit 1; } | ||
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while [[ $# -gt 0 ]] | ||
do | ||
key=$1 | ||
case $key in | ||
-r) | ||
ref=$2 | ||
shift # past argument | ||
shift # past value | ||
;; | ||
-m) | ||
memory=$2 | ||
shift # past argument | ||
shift # past value | ||
;; | ||
esac | ||
done | ||
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if [[ ${ref} == 'hg37' ]]; then | ||
for i in {1..22}; do | ||
echo $i | ||
echo https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.bref3/chr$i.1kg.phase3.v5a.b37.bref3 | ||
wget https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.bref3/chr$i.1kg.phase3.v5a.b37.bref3 | ||
done | ||
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wget https://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.bref3/chrX.1kg.phase3.v5a.b37.bref3 | ||
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wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh37.map.zip | ||
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unzip plink.GRCh37.map.zip | ||
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else | ||
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for i in {1..22}; do | ||
echo $i | ||
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz | ||
(zcat ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz | head -n 300 | grep "#" ; zcat ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz | grep -v "#" | sed 's/^/chr/') | java -Xmx${memory}M -jar beagle.jar > ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.CHR.bref3 | ||
done | ||
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wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chrX.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz | ||
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wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip | ||
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unzip plink.GRCh38.map.zip | ||
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fi | ||
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