Pisces Quick Start 5.2.7 - tamsen/Pisces GitHub Wiki
The Pisces Paper
https://academic.oup.com/bioinformatics/article/35/9/1579/5124278
Please cite us: Tamsen Dunn, Gwenn Berry, Dorothea Emig-Agius, Yu Jiang, Serena Lei, Anita Iyer, Nitin Udar, Han-Yu Chuang, Jeff Hegarty, Michael Dickover, Brandy Klotzle, Justin Robbins, Marina Bibikova, Marc Peeters, Michael Strömberg, Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data, Bioinformatics, Volume 35, Issue 9, 1 May 2019, Pages 1579–1581, https://doi.org/10.1093/bioinformatics/bty849
Data used in paper
https://basespace.illumina.com/s/6vuFN2Cn0Ems
Suggested configuration
Somatic and germline Pisces settings below were used for the Amplicon data in the paper above. The paper results are from Pisces v5.2.5. The ultra low freq command is typically used with a UMI-collapsed BAM, and is included with the caveat that although this will find your variants, it will also call a lot of noise, so further filtering is suggested.
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Somatic: -bam {Bam} -CallMNVs false -g {genome folder} -gVCF false -i {interval file} -OutFolder {outfolder} -RMxNFilter 5,9,0.35
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Germline: -bam {Bam} -CallMNVs false -crushvcf true -g {genome folder} -gVCF false -i {interval file} -ploidy diploid -OutFolder {outfolder} -RMxNFilter 5,9,0.35
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Ultra low freq: -bam {Bam} -g {genome folder} -OutFolder {outfolder} -MinVF 0.0005 -SSFilter false -MinBQ 65 -MaxVQ 100 -MinDepthFilter 500 -MinVQ 0 -VQFilter 20 -ReportNoCalls True -CallMNVs False -RMxNFilter 5,9,0.35 -MinDepth 5 -threadbychr true
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High Speed: (To get results on a exome / WGS bam fast as possible) -bam {Bam} -CallMNVs false -g {genome folder} -gVCF false -OutFolder {outfolder} -ThreadByChr True -FilterDuplicates true -EnableSingleStrandFilter true
Please note that exact syntax might change, version to version. The version-specific commands are directly available from the command line help, or from the version-specific wiki page ie, https://github.com/tamsen/Pisces/wiki/Pisces-5.2.7-Supported-Options.