feat: import of gnomAD SV data into RocksDB (#66)

holtgrewe · web-flow · commit 3fd72ddd835d · 2023-11-22T07:56:03.000Z
diff --git a/Snakefile b/Snakefile
@@ -161,6 +161,10 @@ rule all:
         f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v3}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/helixmtdb-grch37-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/helixmtdb-grch38-{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-sv-exomes-grch37-{DV.exac_cnv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-sv-exomes-grch38-{DV.gnomad_cnv4}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-sv-genomes-grch37-{DV.gnomad_sv}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-sv-genomes-grch38-{DV.gnomad_sv4}+{PV.annonars}/rocksdb/IDENTITY",
         # ----- conservation
         f"output/full/annonars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
@@ -364,6 +368,7 @@ include: "rules/work/annos/strucvars/exac.smk"
 include: "rules/work/annos/strucvars/g1k.smk"
 include: "rules/work/annos/strucvars/gnomad.smk"
 include: "rules/work/annos/strucvars/clinvar.smk"
+include: "rules/work/annos/strucvars/gnomad_sv4.smk"
 # -- output directory ---------------------------------------------------------------------------
 # ---- mehari
 include: "rules/output/mehari/freqs.smk"
@@ -378,6 +383,7 @@ include: "rules/output/annonars/dbsnp.smk"
 include: "rules/output/annonars/gnomad_exomes.smk"
 include: "rules/output/annonars/gnomad_genomes.smk"
 include: "rules/output/annonars/gnomad_mtdna.smk"
+include: "rules/output/annonars/gnomad_sv.smk"
 include: "rules/output/annonars/helix.smk"
 include: "rules/output/annonars/genes.smk"
 # ---- worker
diff --git a/download_urls.yml b/download_urls.yml
@@ -1,3 +1,47 @@
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz
+  excerpt_strategy:
+    strategy: gz-head
+    count: 225
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.controls_only.sites.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.nonneuro.sites.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/exome_cnv/gnomad.v4.0.cnv.all.vcf.gz
+  excerpt_strategy:
+    strategy: gz-head
+    count: 160
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/exome_cnv/gnomad.v4.0.cnv.non_neuro.vcf.gz
+  excerpt_strategy:
+    strategy: gz-head
+    count: 160
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/exome_cnv/gnomad.v4.0.cnv.non_neuro_controls.vcf.gz
+  excerpt_strategy:
+    strategy: gz-head
+    count: 160
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr1.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr2.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr3.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr4.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr5.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr6.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr7.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr8.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr9.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr10.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr11.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr12.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr13.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr14.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr15.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr16.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr17.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr18.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr19.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr20.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr21.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chr22.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chrX.vcf.gz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/4.0/genome_sv/gnomad.v4.0.sv.chrY.vcf.gz
+
 - url: https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz
 
 - url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv
@@ -204,7 +248,6 @@
 - url: http://dgv.tcag.ca/dgv/docs/DGV.GS.hg38.gff3
 - url: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/cnv/exac-final.autosome-1pct-sq60-qc-prot-coding.cnv.bed
 - url: https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/integrated_sv_map/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz
-- url: https://storage.googleapis.com/gcp-public-data--gnomad/papers/2019-sv/gnomad_v2.1_sv.sites.vcf.gz
 
 - url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.1.vcf.bgz
 - url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.2.vcf.bgz
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diff --git a/excerpt-data/0be9b2561c9397f2/gnomad.v4.0.sv.chr15.vcf.gz b/excerpt-data/0be9b2561c9397f2/gnomad.v4.0.sv.chr15.vcf.gz
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