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.
  

• CADD Github page

• Module Name: CADD (see the modules page for more information)
• Use "-m" for v1.7.2 because the singularity size is over 8G!
• Better to use input in vcf.gz format instead of vcf file
• Unusual environment variables set
  • CADD_HOME  CADD installation directory
  • CADD_BIN       CADD executable directory
  • CADD_DATA   CADD data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4206 ~]$ module load cadd 
[+] Loading CADD 1.7.2 on cn4206
[user@cn4206 ~]$ which CADD.sh
/usr/local/apps/CADD/1.6.post1/bin/CADD
user@cn4206 ~]$ CADD.sh -h
CADD.sh [-o ] [-g ] [-v ] [-a]   -- CADD version 1.7

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 v1.7 possible with this set of scripts [default: v1.7])
    -a  include annotation in output
        input vcf of vcf.gz file (required)
    -m  use conda only (no apptainer/singularity)
    -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.sh -m -c 8 -o my_out.tsv.gz -g GRCh38 $CADD_TEST/input.vcf.gz
CADD-v1.7 (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.hcpAUyYXLv/input.tsv.gz --sdm conda --conda-prefix /usr/local/apps/CADD/1.7.2/CADD-scripts-1.7.2/envs/conda --cores 8 --configfile /usr/local/apps/CADD/1.7.2/CADD-scripts-1.7.2/config/config_GRCh38_v1.7.yml --snakefile /usr/local/apps/CADD/1.7.2/CADD-scripts-1.7.2/Snakefile -q
Assuming unrestricted shared filesystem usage.
host: cn0009
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however important for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Singularity containers: ignored
Job stats:
job           count
----------  -------
decompress        1
join              1
prepare           1
prescore          1
total             4

Select jobs to execute...
Execute 1 jobs...

[user@cn4206 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$