diff --git a/ggd-recipes/GRCh37/dbsnp.yaml b/ggd-recipes/GRCh37/dbsnp.yaml index afe8cc00..5a7ea611 100644 --- a/ggd-recipes/GRCh37/dbsnp.yaml +++ b/ggd-recipes/GRCh37/dbsnp.yaml @@ -2,20 +2,20 @@ --- attributes: name: dbsnp - version: 149-20161121 + version: 150-20170403 recipe: full: recipe_type: bash recipe_cmds: - | - version=149 + version=150 org=human_9606_b${version}_GRCh37p13 - release=20161121 + release=20170403 url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/All_${release}.vcf.gz mkdir -p variation wget -c -O variation/dbsnp-$version-orig.vcf.gz $url [[ -f variation/dbsnp-$version.vcf.gz ]] || zcat variation/dbsnp-$version-orig.vcf.gz | bgzip -c > variation/dbsnp-$version.vcf.gz tabix -f -p vcf variation/dbsnp-$version.vcf.gz recipe_outfiles: - - variation/dbsnp-149.vcf.gz - - variation/dbsnp-149.vcf.gz.tbi \ No newline at end of file + - variation/dbsnp-150.vcf.gz + - variation/dbsnp-150.vcf.gz.tbi \ No newline at end of file diff --git a/ggd-recipes/hg19/dbsnp.yaml b/ggd-recipes/hg19/dbsnp.yaml deleted file mode 100644 index de7d53d8..00000000 --- a/ggd-recipes/hg19/dbsnp.yaml +++ /dev/null @@ -1,21 +0,0 @@ -# UCSFify name sed magic from: https://github.com/mmarchin/utilities/blob/master/ucscify.sh ---- -attributes: - name: dbsnp - version: 149-20161121 -recipe: - full: - recipe_type: bash - recipe_cmds: - - | - version=149 - org=human_9606_b${version}_GRCh37p13 - release=20161121 - url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/archive/All_${release}.vcf.gz - mkdir -p variation - 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-149.vcf.gz - - variation/dbsnp-149.vcf.gz.tbi \ No newline at end of file diff --git a/ggd-recipes/hg19/dbsnp.yaml b/ggd-recipes/hg19/dbsnp.yaml new file mode 120000 index 00000000..10d84de1 --- /dev/null +++ b/ggd-recipes/hg19/dbsnp.yaml @@ -0,0 +1 @@ +../GRCh37/dbsnp.yaml \ No newline at end of file diff --git a/ggd-recipes/hg38/clinvar.yaml b/ggd-recipes/hg38/clinvar.yaml index aef3badd..f0f37278 100644 --- a/ggd-recipes/hg38/clinvar.yaml +++ b/ggd-recipes/hg38/clinvar.yaml @@ -4,13 +4,13 @@ --- attributes: name: clinvar - version: 20170130 + version: 20170404 recipe: full: recipe_type: bash recipe_cmds: - | - release=20170130 + release=20170404 baseurl=ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive/2017/clinvar_${release}.vcf.gz mkdir -p variation wget -c -O variation/clinvar-orig.vcf.gz $baseurl diff --git a/ggd-recipes/hg38/dbsnp.yaml b/ggd-recipes/hg38/dbsnp.yaml index 93778a86..6082136d 100644 --- a/ggd-recipes/hg38/dbsnp.yaml +++ b/ggd-recipes/hg38/dbsnp.yaml @@ -4,20 +4,20 @@ --- attributes: name: dbsnp - version: 149-20161122 + version: 150-20170403 recipe: full: recipe_type: bash recipe_cmds: - | - version=149 - org=human_9606_b${version}_GRCh38p2 - release=20161122 + version=150 + org=human_9606_b${version}_GRCh38p7 + release=20170403 url=ftp://ftp.ncbi.nih.gov/snp/organisms/$org/VCF/All_${release}.vcf.gz mkdir -p variation wget -c -O variation/dbsnp-$version-orig.vcf.gz $url [[ -f variation/dbsnp-$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-149.vcf.gz - - variation/dbsnp-149.vcf.gz.tbi + - variation/dbsnp-150.vcf.gz + - variation/dbsnp-150.vcf.gz.tbi