diff --git a/cre.cloudbiolinux.prepare_gnomad_test.sh b/cre.cloudbiolinux.prepare_gnomad_test.sh index 16192df..9d5b857 100755 --- a/cre.cloudbiolinux.prepare_gnomad_test.sh +++ b/cre.cloudbiolinux.prepare_gnomad_test.sh @@ -2,11 +2,13 @@ # prepares full chomosome test set for gnomad to test ggd recipe mkdir txtmp cd txtmp -prefix=gnomad.exomes.r2.1.sites.grch38.chr +type="genomes" +prefix=gnomad.$type.r2.1.sites.chr +# Y is absent for gnomad genomes for chrom in $(seq 1 22;echo X Y) do - curl -r 0-1000000 -O http://ftp.ensemblorg.ebi.ac.uk/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/exomes/${prefix}${chrom}_noVEP.vcf.gz - gunzip -c ${prefix}${chrom}_noVEP.vcf.gz | head -n 1400 > ${prefix}${chrom}_noVEP.vcf + curl -r 0-1000000 -O http://ftp.ensemblorg.ebi.ac.uk/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/${type}/${prefix}${chrom}_noVEP.vcf.gz + gunzip -c ${prefix}${chrom}_noVEP.vcf.gz | head -n 1200 > ${prefix}${chrom}_noVEP.vcf bgzip -f ${prefix}${chrom}_noVEP.vcf tabix ${prefix}${chrom}_noVEP.vcf.gz done