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-observationsprosic-callprosic-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:
Further, the PROSIC depends on the following Python packages:
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.