Pisces is a small variant calling application, tuned for amplicons and enrichment panels. By default, it calls low frequency somatic variants on tumor-only samples, but it also supports germline calling. It is included with the Illumina MiSeqReporter pipeline and various BaseSpace workflows. The caller can also be run as a standalone program. Pisces is a "software suite" that has several executables:
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Stitcher - Stitches two paired-end reads together into a single read
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Pisces - Calls small variants
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Scylla - Detects multiple nucleotide variants (MNVs) in a given sample and phases the variants in complex regions into sub populations
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VariantQualityRecalibration - Recalibrates the variant quality scores (Q scores) if the particular variants are over represented
POC: Tamsen Dunn and Gwenn Berry
Pisces source code is provided under the GPLv3 license. Pisces includes third party packages provided under other open source licenses, please see COPYRIGHT.txt for additional details.
Strelka is available for matched tumor/normal variant calling, and is part of the TUNE workflow secondary analysis workflow. http://www.ncbi.nlm.nih.gov/pubmed/22581179
64 bit OS.
If running on windows, you need .net framework 4.5.1. This is freely available from http://www.microsoft.com/download/en/details.aspx?id=21
If running on Linux, you need mono installed and the “libFileCompression.so” file included with the Pisces solution. Mono is freely available from http://www.mono-project.com/docs/about-mono/releases/ . We typically use mono-3.10.0
Latest distributions are available at: https://github.com/Illumina/Pisces/tree/release/Pisces_5_1_6/redist
So long as mono (for Linux) or .NET (for Windows) has been installed, the uncompressed binary is ready to go. Example command lines are:
Windows:
Pisces.exe -B C:\my\path\to\TestData\example_S1.bam -g C:\my\path\to\WholeGenomeFasta -MinVF 0.01
Linux:
mono Pisces.exe -B /my/path/to/TestData/example_S1.bam -g /my/path/to/WholeGenomeFasta -MinVF 0.01
example qsub cmd to a grid cluster:
echo "Pisces.exe -B /path/to/mybam.bam -g /Genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta -MinVF 0.01" | qsub -N PISCESJob -pe threaded 16-20 -M you@yoursmtp.com -m eas
It is necessary to supply a reference genome following the -g argument. Reference genomes may be downloaded from illumina's website at: http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn
Note, the main executable Pisces.exe was originally named CallSomaticVariants.exe. So the above commands need to be altered for the 5.0.x releases.
To configure and install, build the solution and copy the build to the desired location. The build is a windows process, and the solution in this repository is for VisualStudio 2015. Load the solution into VS, and build in release, x64 mode. This will create a bin\x64\Release folder along side the solution file. The Release folder has everything needed to run on windows and linux (under mono). To run unit tests, be sure to configure your Default Processor Architecture in VS to x64 (else you will hit BadImageFormatExceptions).
The component algorithms are intended for developers to re-use and improve them. This version is not commercially supported and provided as is under the GNU GENERAL PUBLIC LICENSE. For first time use, we recommend testing with the example in the "testdata" folder.
https://github.com/Illumina/Pisces/wiki
https://github.com/Illumina/Pisces/wiki/Frequently-Asked-Questions