Patchwork
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Application data |
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| Created by | Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson |
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| Biological application domain(s) | Structural variation, Copy number estimation |
| Technology | ABI SOLiD, Illumina, Complete Genomics |
| Created at | Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751
85 Uppsala, Sweden |
| Maintained? | Yes |
| Input format(s) | BAM, Pileup, VCF |
| Output format(s) | PNG, JPG, CSV |
| Software features | Allele specific copy numbers. |
| Programming language(s) | R |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Operating system(s) | Linux, Mac OS X |
Summary: 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 in two formats. The first, named simply patchwork, takes BAM files as input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be found in their respective tabs.
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References
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