diff --git a/data/download_data.sh b/data/download_data.sh index 1938f924..be7b0eb7 100755 --- a/data/download_data.sh +++ b/data/download_data.sh @@ -143,19 +143,19 @@ mkdir -p $dbs # # # -# download REVEL (https://sites.google.com/site/revelgenomics/downloads) -cd $dbs -mkdir -p REVEL -cd REVEL -source $tools/zhead.sh -#old url: wget https://rothsj06.u.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip -wget https://rothsj06.dmz.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip -unzip -p revel-v1.3_all_chromosomes.zip | tr ',' '\t' | sed '1s/.*/#&/' | bgzip > revel_tmp.tsv.gz -zhead revel_tmp.tsv.gz 1 > h -zgrep -h -v '^#chr' revel_tmp.tsv.gz | $ngsbits/TsvFilter -numeric -v -filter '3 is .' | egrep -v '^#\s' | sort -k1,1 -k3,3n - | cat h - > revel_grch38_all_chromosomes.tsv -python3 $tools/db_converter_revel.py -i revel_grch38_all_chromosomes.tsv | $ngsbits/VcfLeftNormalize -stream -ref $genome | $ngsbits/VcfStreamSort | bgzip -c > revel_grch38_all_chromosomes.vcf.gz -tabix -f -p vcf revel_grch38_all_chromosomes.vcf.gz -rm -f revel_tmp.tsv.gz h revel_grch38_all_chromosomes.tsv +# download REVEL (https://sites.google.com/site/revelgenomics/downloads) https://download.imgag.de/ahdoebm1/revel_grch38_all_chromosomes.vcf.gz +#cd $dbs +#mkdir -p REVEL +#cd REVEL +#source $tools/zhead.sh +##old url: wget https://rothsj06.u.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip +#wget https://rothsj06.dmz.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip +#unzip -p revel-v1.3_all_chromosomes.zip | tr ',' '\t' | sed '1s/.*/#&/' | bgzip > revel_tmp.tsv.gz +#zhead revel_tmp.tsv.gz 1 > h +#zgrep -h -v '^#chr' revel_tmp.tsv.gz | $ngsbits/TsvFilter -numeric -v -filter '3 is .' | egrep -v '^#\s' | sort -k1,1 -k3,3n - | cat h - > revel_grch38_all_chromosomes.tsv +#python3 $tools/db_converter_revel.py -i revel_grch38_all_chromosomes.tsv | $ngsbits/VcfLeftNormalize -stream -ref $genome | $ngsbits/VcfStreamSort | bgzip -c > revel_grch38_all_chromosomes.vcf.gz +#tabix -f -p vcf revel_grch38_all_chromosomes.vcf.gz +#rm -f revel_tmp.tsv.gz h revel_grch38_all_chromosomes.tsv #$ngsbits/VcfCheck -in revel_grch38_all_chromosomes.vcf.gz -ref $genome -lines 0 # #