Patchwork

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Name Patchwork
Description Patchwork: Bioinformatic tool for allele-specific copynumber analysis of tumor samples
Project financing   SNIC/SciLifeLab
Is active yes
Start date 2012-06-01
End date 2013-10-01

Patchwork is a bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid.

Patchwork is available for two data types. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files.

http://patchwork.r-forge.r-project.org/

Publication: http://genomebiology.com/2013/14/3/R24/abstract

Members

Centre Role Field
Sebastian DiLorenzo (UPPMAX) UPPMAX Application expert Bioinformatics
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