SomaticSeq is an ensemble approach to accurately detect somatic mutations. It incorporates multiple somatic mutation caller(s) to obtain a combined call set, and then uses machine learning to distinguish true mutations from false positives from that call set.
References:
- Li Tai Fang, Pegah Tootoonchi Afshar, Aparna Chhibber, Marghoob Mohiyuddin, Yu Fan, John C. Mu, Greg Gibeling, Sharon Barr, Narges Bani Asadi, Mark B. Gerstein, Daniel C. Koboldt, Wenyi Wang, Wing H. Wong, and Hugo Y.K. Lam. An Ensemble Approach to Accurately Detect Somatic Mutations Using SomaticSeq. Genome Biology, 16(1):197. (2015). DOI: 10.1186/s13059-015-0758-2
There may be multiple versions of SomaticSeq available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail SomaticSeq
To select a module, type
module load SomaticSeq/[ver]
where [ver] is the version of choice.
Environment variables set:
- $PATH
- $SOMATICSEQ_HOME
The SomaticSeq wrapper script requires GATK, which cannot be used on Helix.
Create a swarmfile following the swarm guide using the example commands on this page.
Create a batch input file (e.g. somaticseq.sh). For example:
#!/bin/bash module load SomaticSeq mkdir results SomaticSeq.Wrapper.sh \ --snpeff-dir "$SNPEFF_JARPATH" \ --gatk "$GATK_HOME" \ --ada-r-script "$SOMATICSEQ_HOME/r_scripts/ada_model_builder.R" \ --genome-reference /fdb/genome/human-feb2009/hg19.fa \ --output-dir results \ --normal-bam <normal.bam> \ --tumor-bam <tumor.bam> \ ... (additional parameters) ...
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=1 somaticseq.sh
- SomaticSeq Main Site: http://bioinform.github.io/somaticseq/
