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Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

ABSTRACT: Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-project.org/).

SUBMITTER: Mayrhofer M 

PROVIDER: S-EPMC4053982 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

Mayrhofer Markus M   DiLorenzo Sebastian S   Isaksson Anders A  

Genome biology 20130325 3

Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell cont  ...[more]

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