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Old 04-16-2012, 10:13 PM   #1
mackan
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Default Patchwork - allele-specific somatic CNAs in cancer (WGS)

We have developed an R package for allele-specific copy number analysis of whole genome sequenced tumor tissue, capable of handling normal cell content and aneuploidy. The software takes BAM or ASM (Complete Genomics) formatted input, and is designed for difficult samples with low tumor cell content or coverage, subclones, or complex genomic alterations such as chromothripsis.

Instructions are under development and available at:
http://patchwork.r-forge.r-project.org/

The R package is hosted at:
https://r-forge.r-project.org/projects/patchwork/

Some aspects of the code remain a work in progress, and there may be a few bugs around. Feel free to contact us (or post here) with any feedback or questions.
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Old 04-19-2012, 03:04 AM   #2
colindaven
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Does it also work with haploid organisms, eg bacteria ?
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Old 04-19-2012, 04:54 AM   #3
mackan
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Quote:
Originally Posted by colindaven View Post
Does it also work with haploid organisms, eg bacteria ?
Human genomes only at this time, we have no plans for other species.
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allele frequency, cancer, copy number, loh, whole genome sequencing

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