GBScleanR: GBScleanR: A package to conduct error correction for noisy...
In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data
GBScleanR R Documentation
GBScleanR: A package to conduct error correction for noisy genotyping by
sequencing (reduced representation sequencing based genotyoing) data.
Description
GBScleanR is a package for quality check, filtering, and error correction of
genotype data derived from next generation sequcener (NGS) based genotyping
platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main
function of this package is "clean.geno" which estimates the true genotypes
of samples from given read counts for genotype markers using a hidden Markov
model with incorporating uneven observation ratio of allelic reads. This
implementation gives robust genotype estimation even in noisy genotype data
usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g.
RADseq. GBScleanR currenly only supports genotype data of
biparental populations.
Author(s)
Maintainer: Tomoyuki Furuta f.tomoyuki@okayama-u.ac.jp (ORCID)
See Also
Useful links:
tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.
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| GBScleanR | R Documentation |
GBScleanR: A package to conduct error correction for noisy genotyping by sequencing (reduced representation sequencing based genotyoing) data.
Description
GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is "clean.geno" which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. GBScleanR currenly only supports genotype data of biparental populations.
Author(s)
Maintainer: Tomoyuki Furuta f.tomoyuki@okayama-u.ac.jp (ORCID)
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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