gnomad_test

naumenko-sa · May 11, 2019 · aa7ed1d · aa7ed1d
1 parent e5863a5
commit aa7ed1d
Showing 1 changed file with 5 additions and 3 deletions.
diff --git 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