gsutil cp gs://gcp-public-data--gnomad/release/4.1/vcf/joint/* .
gnomAD scripts updated and ran again:
- make-gnomad-af-file.sh
- convert-gnomad-to-csv.sh
The annotations in gnomAD now contain joint allele frequencies with both WES and WGS. The VCF fields added by vcfanno are now named: gnomadAF_joint, gnomadAF_joint_grpmax, gnomadAF_genomes. The grpmax field is the AF in the genetic ancestry group with the highest AF. vcfanno_config.toml and vcfanno_resources_template.txt updated with new gnomAD.
New resource files:
- gnomad.joint.v4.1.sites.af.vcf.bgz
- gnomad.joint.v4.1.sites.af.vcf.bgz.tbi
- gnomad.joint.v4.1.af.tab.gz
There is no new gnomAD for chrM.
gnomAD SV has been updated from gnomAD 2 to 4.1. See README file for the dataset used.
I was not able to get it to work. Staying on version 1.6.post1.
- Downloaded pre-scored SNP vcf files https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz
- Updated vcfanno_resources.txt to point to CADD 1.7 SNP files
- vcfanno config is changed to report the "max" CADD score for a site instead of "mean". It probably won't make a difference because there will only be one CADD score per variant.
- Downloaded annotation data for off-line use: https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/GRCh38_v1.7.tar.gz
- (TODO= Updating CADD itself)
Downloaded https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/variant_catalog_grch38.json on 2024-04-15, commit 648e527.
See also below about how the files were restructured due to pipeline changes. New VEP cache is downloaded. See README file.
ClinVar was updated on 2024-09-19, by downloading the current clinvar files.
The same SpiceAI files are used.
- variant_consequences_v2.txt (new required file)
-
mobile_element_svdb_annotations: No ref data were downloaded for this yet, the gnomad SV files were used instead.
-
vep plugin files moved from vep_cache to vep_files:
LoFtool_scores.txt, pLI_values.txt, spliceai*.
New file vep_files_template.csv created (instanciable with make-absolute-paths.sh)
-
nextflow updated to 24.04.4 (TODO confirm version in prod)