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Single nucleotide variant (SNV) expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

Reference:

• Jones, D., Raine, K.M., Davies, H., Tarpey, P., Butler, A.P., Teague, J.W., Nik-Zainal, S., and Campbell, P.J.
  cgpCaVEManWrapper: Simple execution of CaVEMan in order to detect somatic single nucleotide variants in NGS data.
  Curr. Protoc. Bioinform., 2016, 56: 15.10.1-15.10.18; doi: 10.1002/cpbi.20

• caveman Main Site

• Module Name: caveman (see the modules page for more information)
• Singlethreaded
• Sample data in /usr/local/apps/caveman/test_data
• Unusual environment variables set
  • CAVEMAN_HOME  installation directory
  • CAVEMAN_BIN       executable directory
  • CAVEMAN_DATA  sample testing data

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load caveman

[user@cn3144 ~]$ mkdir /data/$USER/caveman; cd /data/$USER/caveman

Copy sample data to the current folder:

[user@cn3144 ~]$ cp -r $CAVEMAN_DATA . 

This command will create a data folder test_data in the current directory. Processing of the data by cavemen can be performed in five steps described in the documentation and reproduced below.

Step 1:

[user@cn3144 ~]$ caveman setup -t test_data/test_mt.bam -n test_data/test_wt.bam -r test_data/genome.fa.fai -g test_data/ign.test

- files ./caveman.cfg.ini and ./alg_bean will be produced in the current directory.

Step 2:

[user@cn3144 ~]$ caveman split -i 1

- file ./splitList.1 will be produced.

For the further processing, the name of the splitList file should be the same as specified in the file ./caveman.cfg.ini, so one should either to
- edit the file ./caveman.cfg.ini accordinglty, or
- store the contents of the file(s) splitList.* in a file splitList:

[user@cn3144 ~]$ cat ./splitList.* > splitList

Step 3:

[user@cn3144 ~]$ caveman mstep -i 1

Folder ./results/1 will be created.

Step 4:

[user@cn3144 ~]$ caveman merge

- files probs_arr and covs_arr will be created in the current folder.

Step 5:

[user@cn3144 ~]$ caveman estep -i 1  -v 37/GRCh37  -w human

More files will be produced in the folder results/1. Note that specifying the options -v and -w is obligatory for this step.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. caveman.sh). For example:

#!/bin/bash
set -e
module load caveman
for i in {1..2}; do
      caveman split -i $i
done
cat splitList.? > splitList
for i in {1..2}; do
      caveman mstep -i $i
done
caveman merge
for i in {1..2}; do
      caveman estep -i $i
done

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#g] caveman.sh