feat: integrating gnomAD v4 (#75)

varfish-org · Dec 29, 2023 · d529d7e · d529d7e
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Showing 258 changed files with 992 additions and 49 deletions.
diff --git a/Snakefile b/Snakefile
@@ -122,8 +122,8 @@ rule all:
         f"work/download/annos/grch37/seqvars/dbsnp/{DV.dbsnp}/dbsnp.vcf.gz",
         f"work/annos/grch38/seqvars/helixmtdb/{DV.helixmtdb}/helixmtdb.vcf.gz",
         f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
-        f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done",
-        f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v3}/.done",
+        f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v4}/.done",
+        f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v4}/.done",
         # NB: gnomAD-SV GRCh38 was announced end of 2020 but not released yet
         # -- genome browser "features" (position-specific)
         # ---- GRCh37
@@ -140,7 +140,7 @@ rule all:
         # -- mehari data
         # ---- frequencies (via annonars)
         f"output/full/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/full/mehari/freqs-grch38-{DV.gnomad_v3}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
         # -- annonars data
         # ----- sequence variant annotations
         f"output/full/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
@@ -156,9 +156,9 @@ rule all:
         f"output/full/annonars/gnomad-mtdna-grch37-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/gnomad-mtdna-grch38-{DV.gnomad_mtdna}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/full/annonars/gnomad-exomes-grch38-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/full/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v3}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/full/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{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",
@@ -286,12 +286,12 @@ rule all:
         f"output/reduced-dev/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v3}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
         # -- mehari
         f"output/reduced-dev/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v3}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-dev/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
         #
         # == exomes (reduced data) directories ==================================================
         #
@@ -318,12 +318,12 @@ rule all:
         f"output/reduced-exomes/annonars/dbscsnv-grch37-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/dbscsnv-grch38-{DV.dbscsnv}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/gnomad-exomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-exomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/gnomad-genomes-grch37-{DV.gnomad_v2}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v3}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/annonars/gnomad-genomes-grch38-{DV.gnomad_v4}+{PV.annonars}/rocksdb/IDENTITY",
         # -- mehari
         f"output/reduced-exomes/mehari/freqs-grch37-{DV.gnomad_v2}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
-        f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v3}+{DV.gnomad_v2}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
+        f"output/reduced-exomes/mehari/freqs-grch38-{DV.gnomad_v4}+{DV.gnomad_v4}+{DV.gnomad_mtdna}+{DV.helixmtdb}+{PV.annonars}/rocksdb/IDENTITY",
 
 
 # ===============================================================================================

diff --git a/download_urls.yml b/download_urls.yml
@@ -87,11 +87,11 @@
     strategy: no-excerpt
     count: null
 
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.3.0/mehari-data-txs-grch37-0.3.0.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch37-0.4.4.bin.zst
   excerpt_strategy:
     strategy: no-excerpt
     count: null
-- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.3.0/mehari-data-txs-grch38-0.3.0.bin.zst
+- url: https://github.com/bihealth/mehari-data-tx/releases/download/v0.4.4/mehari-data-txs-grch38-0.4.4.bin.zst
   excerpt_strategy:
     strategy: no-excerpt
     count: null
@@ -213,6 +213,7 @@
     count: null
 
 - url: https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz
+- url: https://storage.googleapis.com/gcp-public-data--gnomad/release/v4.0/constraint/gnomad.v4.0.constraint_metrics.tsv
 - url: https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen
 
 - comment: We replace the linux64.gene2.xml binary with a wrapper to zcat...
@@ -258,6 +259,106 @@
 - 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://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr1.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr2.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr3.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr4.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr5.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr6.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr7.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr8.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr9.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr10.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr11.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr12.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr13.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr14.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr15.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr16.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr17.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr18.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr19.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr20.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr21.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr22.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chrX.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chrY.vcf.bgz
+
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr1.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr2.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr3.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr4.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr5.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr6.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr7.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr8.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr9.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr10.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr11.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr12.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr14.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr15.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr16.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr17.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr18.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr19.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr20.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chr22.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chrX.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/exomes/gnomad.exomes.v4.0.sites.chrY.vcf.bgz.tbi
+
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr2.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr3.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr4.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr5.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr6.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr7.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr8.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr9.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr10.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr11.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr12.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr13.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr14.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr15.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr16.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr17.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr18.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr19.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr20.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr21.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr22.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chrX.vcf.bgz
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chrY.vcf.bgz
+
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr2.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr3.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr4.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr5.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr6.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr7.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr8.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr9.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr10.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr11.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr12.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr13.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr14.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr15.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr16.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr17.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr18.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr19.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr20.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr21.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr22.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chrX.vcf.bgz.tbi
+- url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chrY.vcf.bgz.tbi
+
 - 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
 - url: https://gnomad-public-us-east-1.s3.amazonaws.com/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.3.vcf.bgz

diff --git a/environment.yml b/environment.yml
@@ -41,9 +41,9 @@ dependencies:
   # Parallel (de)compression.
   - pigz
   # Varfish related
-  - annonars =0.28.0
-  - viguno =0.1.6
-  - mehari =0.18.1
-  - varfish-server-worker =0.10.1
+  - annonars =0.32.0
+  - viguno =0.2.0
+  - mehari =0.21.1
+  - varfish-server-worker =0.10.2
   # S3 uploads
   - s5cmd =2.1.0
diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz
diff --git a/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi b/excerpt-data/0106e2c5435e5972/gnomad.exomes.v4.0.sites.chr13.vcf.bgz.tbi
diff --git a/excerpt-data/0106e2c5435e5972/url.txt b/excerpt-data/0106e2c5435e5972/url.txt
diff --git a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz b/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz
diff --git a/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi b/excerpt-data/03c9dba47d8d1fbc/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi
diff --git a/excerpt-data/03c9dba47d8d1fbc/url.txt b/excerpt-data/03c9dba47d8d1fbc/url.txt
diff --git a/excerpt-data/05d48443127f19c1/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi b/excerpt-data/05d48443127f19c1/gnomad.exomes.v4.0.sites.chr21.vcf.bgz.tbi
diff --git a/excerpt-data/05d48443127f19c1/url.txt b/excerpt-data/05d48443127f19c1/url.txt