CADD: scoring the deleteriousness of SNPs and indels in the Human Genome.
CADD (Combined Annotation Dependent Depletion) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. Currently, it supports the builds: GRCh37/hg19 and GRCh38/hg38.
References:
- Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper & Jay Shendure
A general framework for estimating the relative pathogenicity of human genetic variants.
Nature Genetics 2014 Feb 2. doi: 10.1038/ng.2892. - Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M.
CADD: predicting the deleteriousness of variants throughout the human genome.
Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky1016.
Documentation
Important Notes
- Module Name: CADD (see the modules page for more information)
- Unusual environment variables set
- CADD_HOME CADD installation directory
- CADD_BIN CADD executable directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn4206 ~]$ module load cadd [+] Loading snakemake 6.5.3 [+] Loading CADD 1.6.post1 on cn4206 [user@cn4206 ~]$ which CADD /usr/local/apps/CADD/1.6.post1/bin/CADD user@cn4206 ~]$ CADD -h CADD [-oEnd the interactive session:] [-g ] [-v ] [-a] -- CADD version 1.6 where: -h show this help text -o out tsv.gz file (generated from input file name if not set) -g genome build (supported are GRCh37 and GRCh38 [default: GRCh38]) -v CADD version (only v1.6 possible with this set of scripts [default: v1.6]) -a include annotation in output input vcf of vcf.gz file (required) -q print basic information about snakemake run -p print full information about the snakemake run -c number of cores that snakemake is allowed to use [default: 1] [user@cn4206 ~]$ CADD -o my_out.tsv.gz /fdb/CADD/1.6.post1/test/input.vcf CADD-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved. OUTFILE=my_out.tsv.gz Running snakemake pipeline: snakemake /tmp/tmp.jfNNBZaoNk/input.tsv.gz --use-conda --conda-prefix /vf/db/CADD/1.6.post1/envs --cores 1 --configfile /vf/db/CADD/1.6.post1/config/config_GRCh38_v1.6_noanno.yml --snakefile /vf/db/CADD/1.6.post1/Snakefile -q Job stats: job count min threads max threads ---------- ------- ------------- ------------- annotation 1 1 1 imputation 1 1 1 join 1 1 1 prepare 1 1 1 prescore 1 1 1 score 1 1 1 total 6 1 1 Opening /vf/db/CADD/1.6.post1/data/prescored/GRCh38_v1.6/no_anno/gnomad.genomes.r3.0.indel.tsv.gz... Opening /vf/db/CADD/1.6.post1/data/prescored/GRCh38_v1.6/no_anno/whole_genome_SNVs.tsv.gz... Possible precedence issue with control flow operator at /vf/db/CADD/1.6.post1/envs/e507b9d6fe0a5d0ae12148a5d819bc0e/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805. CADD scored variants written to file: my_out.tsv.gz [user@cn4206 ~]$ CADD -o my_out.tsv.gz -g GRCh37 /fdb/CADD/1.6.post1/test/input.vcf CADD-v1.6 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health 2013-2020. All rights reserved. Running snakemake pipeline: snakemake /tmp/tmp.scK9I9hCpe/input.tsv.gz --use-conda --conda-prefix /vf/db/CADD/1.6.post1/envs --cores 1 --configfile /vf/db/CADD/1.6.post1/config/config_GRCh37_v1.6_noanno.yml --snakefile /vf/db/CADD/1.6.post1/Snakefile -q Job stats: job count min threads max threads ---------- ------- ------------- ------------- annotation 1 1 1 imputation 1 1 1 join 1 1 1 prepare 1 1 1 prescore 1 1 1 score 1 1 1 total 6 1 1 Opening /vf/db/CADD/1.6.post1/data/prescored/GRCh37_v1.6/no_anno/InDels.tsv.gz... Opening /vf/db/CADD/1.6.post1/data/prescored/GRCh37_v1.6/no_anno/whole_genome_SNVs.tsv.gz... Possible precedence issue with control flow operator at /vf/db/CADD/1.6.post1/envs/e507b9d6fe0a5d0ae12148a5d819bc0e/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805. CADD scored variants written to file: my_out.tsv.gz
[user@cn4206 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$