Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.
Genome Biol
; 14(3): R24, 2013 Mar 25.
Article
in En
| MEDLINE
| ID: mdl-23531354
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/).
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Genome, Human
/
Sequence Analysis, DNA
/
Computational Biology
/
Alleles
/
DNA Copy Number Variations
/
Neoplasms
Limits:
Female
/
Humans
Language:
En
Journal:
Genome Biol
Journal subject:
BIOLOGIA MOLECULAR
/
GENETICA
Year:
2013
Document type:
Article