Prosic has been succeeded by Varlociraptor. Please use Varlociraptor instead.

PROSIC is available via Bioconda, a distribution of bioinformatics software for the conda package manager. Bioconda can be set up in any Linux environment, even without admin rights. With Bioconda set up, PROSIC can be installed via

$ conda install prosic

PROSIC offers three command line utilities:

• prosic-extract-observations
• prosic-call
• prosic-annotate

The purpose of PROSIC is to call somatic insertions and deletions (indels) on tumor/normal sample pairs. For this, PROSIC requires a VCF file with preliminary indel calls, e.g. obtained with Platypus. Then, calling with PROSIC consists of three steps.

First, we extract informations about relevant variants and the corresponding alignments from the VCF and the corresponding BAM files:

$ prosic-extract-observations $ALIGNER pre-calls.vcf normal.bam tumor.bam > observations.txt

See prosic-extract-observations --help for information about the valid values of $ALIGNER and other parameters.

Second, the significance of mutations is assessed via

$ prosic-call observations.txt > calls.txt

See prosic-call -h for information about parameters.

Finally, the initial VCF file is annotated with the somatic mutation calls from PROSIC:

$ prosic-annotate pre-calls.vcf calls.txt > calls.vcf

Thereby, each indel in the resulting VCF is classified into CALL=SOMATIC or CALL=GERMLINE and the posterior probability for the selected event is provided in the field POSTERIOR_PROB.

PROSIC uses the following C libraries:

• The GNU scientific library (GSL)
• The GMP library for arbitrary precision arithmetic

Further, the PROSIC depends on the following Python packages:

• PySAM for working with BAM/SAM files
• PyVCF for working with VCF files

To install PROSIC from source, issue the following commands:

$ cmake CMakeLists.txt && make
$ cp bin/prosic-call $BIN_PATH
$ python setup.py install --user

Where $BIN_PATH should be a folder in your $PATH, e.g. ~/.local/bin.

Louis Dijkstra