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CNValidator: validating somatic copy-number inference.

ABSTRACT:

Motivation

CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values.

Results

On a dataset of somatic samples from individuals with Barrett's Esophagus, CNValidator provided feedback on the correctness of sample ploidy calls and also detected data quality issues.

Availability and implementation

CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Smith LP

PROVIDER: S-EPMC6662281 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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CNValidator: validating somatic copy-number inference.

Smith Lucian P LP Yamato Jon A JA Kuhner Mary K MK

Bioinformatics (Oxford, England) 20190801 15

<h4>Motivation</h4>CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values.<h4>Results</h4>On a dataset of somatic samples from individuals with Barret ...[more]

PMID: 30541069

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