Biowulf High Performance Computing at the NIH
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:

Documentation
Important Notes

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 [-o ] [-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
End the interactive session:
[user@cn4206 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$