From a66cb1de9004ac93b02f61342177787bbbfa2234 Mon Sep 17 00:00:00 2001 From: zhaoxiaofei Date: Mon, 23 May 2022 16:40:11 +0800 Subject: [PATCH] Added code for downloading and preparing the HNF4A dataset. Used version 6f045940ff8f694270ee16a4fd6fb3cf0a667cb4 of UVC-delins. --- install-dependencies.sh | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/install-dependencies.sh b/install-dependencies.sh index 3ddee25..67e77ce 100755 --- a/install-dependencies.sh +++ b/install-dependencies.sh @@ -53,7 +53,7 @@ if [ $(echo "${PAT}" | grep -c skip-software) -eq 0 ]; then git clone https://github.com/genetronhealth/uvc-delins.git fi pushd uvc-delins - git checkout f2987d5 + git checkout 6f045940ff8f694270ee16a4fd6fb3cf0a667cb4 bash -evx ./install-dependencies.sh "$skipdown" && make && make deploy && cp bin/* ./ popd @@ -143,5 +143,13 @@ if [ $(echo "${PAT}" | grep -c skip-ref) -eq 0 ]; then zcat dbsnp_138.b37.vcf.gz > dbsnp_138.b37.vcf fi $gatk4lowmem IndexFeatureFile -I dbsnp_138.b37.vcf + +mkdir -p ${EVALROOT}/HNF4A.datadir/ && pushd ${EVALROOT}/HNF4A.datadir/ +getdata https://zenodo.org/record/3375579/files/rdemolgen/MNV-test-data-1_0.zip +unzip MNV-test-data-1_0.zip +cp rdemolgen-MNV-test-data-7902a56/HNF4A.bam HNF4A_12.bam +cp rdemolgen-MNV-test-data-7902a56/HNF4A.bam.bai HNF4A_12.bam.bai +popd + popd