hg38: update to version dbSNP 144 #196

config/biodata.yaml

@@ -28,10 +28,10 @@ genomes:
     annotations: [battenberg]
   - dbkey: hg38
     name: Human (hg38) full
-    annotations: [dbsnp-142, clinvar, mills_indels, 1000g_snps, 1000g_indels, 1000g_omni_snps, hapmap_snps]
+    annotations: [dbsnp, clinvar, mills_indels, 1000g_snps, 1000g_indels, 1000g_omni_snps, hapmap_snps]
   - dbkey: hg38-noalt
     name: Human (hg38) without alternative alleles
-    annotations: [dbsnp-142, clinvar, mills_indels, 1000g_snps, 1000g_indels, 1000g_omni_snps, hapmap_snps]
+    annotations: [dbsnp, clinvar, mills_indels, 1000g_snps, 1000g_indels, 1000g_omni_snps, hapmap_snps]
   - dbkey: mm9
     name: Mouse (mm9)
     dbsnp: true

ggd-recipes/hg38-noalt/dbsnp-142.yaml → ggd-recipes/hg38-noalt/dbsnp.yaml

@@ -1,20 +1,23 @@
-# dbSNP 142: http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/
+# dbSNP 144: http://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/
 # 
 # UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh
 ---
 attributes:
-  name: dbsnp-142
-  version: 20150416-2
+  name: dbsnp
+  version: 144-20150603
 recipe:
   full:
     recipe_type: bash
     recipe_cmds:
       - |
-        version=142
+        version=144
+        org=human_9606_b$version_GRCh38p2
+        release=20150603
+        url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/All_$release.vcf.gz
         mkdir -p variation
-        wget -c -O variation/dbsnp-$version-orig.vcf.gz ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/All_20150416.vcf.gz
+        wget -c -O variation/dbsnp-$version-orig.vcf.gz $url
         [[ -f variation/dbsnp-$version.vcf.gz ]] || zcat variation/dbsnp-$version-orig.vcf.gz | sed "s/^\([0-9]\+\)\t/chr\1\t/g" | sed "s/^MT/chrM/g" | sed "s/^X/chrX/g" | sed "s/^Y/chrY/g" | bgzip -c > variation/dbsnp-$version.vcf.gz
         tabix -f -p vcf variation/dbsnp-$version.vcf.gz
     recipe_outfiles:
-      - variation/dbsnp-142.vcf.gz
-      - variation/dbsnp-142.vcf.gz.tbi
+      - variation/dbsnp-144.vcf.gz
+      - variation/dbsnp-144.vcf.gz.tbi

ggd-recipes/hg38/dbsnp.yaml

@@ -0,0 +1 @@
+../hg38-noalt/dbsnp.yaml