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Lanc-CSV specifications

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Unique identifier OMICS_17448
Name Lanc-CSV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data GWAS summary statistics, reference panel matching the GWAS population, bed files specifying start and end positions of each locus.
Input format BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, MATLAB
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.1
Stability Beta
Maintained No

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Publication for Lanc-CSV

Lanc-CSV citations

 (4)
library_books

Leveraging local ancestry to detect gene gene interactions in genome wide data

2015
BMC Genet
PMCID: 4619349
PMID: 26498930
DOI: 10.1186/s12863-015-0283-z

[…] the impact might be substantial. for example brown et al. reported squared correlation between true and inferred local ancestry of 0.63, and 0.81 for mexican and puerto rican population when using lanc-csv, which had similar results to other methods []. while further analysis might explore such situations, we believe the results described in this study would remain valid. finally, additional […]

library_books

Differential Evolution approach to detect recent admixture

2015
BMC Genomics
PMCID: 4480842
PMID: 26111206
DOI: 10.1186/1471-2164-16-S8-S9

[…] methods, only a few computational tools exist, particularly for analysis of mixed individuals [-]., these methods can be either local (focusing on origin of chromosomal segments), such as lanc-csv [], lamp-ld [], and multimix [], global (average ancestral proportions across the genome), such as admixture [], structure [,], or both, such as hapmix [], lamp [,]. some popular […]

library_books

Inferring ancestry from population genomic data and its applications

2014
Front Genet
PMCID: 4080679
PMID: 25071832
DOI: 10.3389/fgene.2014.00204

[…] with up to four ancestral populations. presented a two-layer hmm to detect structure of local haplotypes and demonstrated its utility for la inference for both two-way and three-way admixture. lanc-csv (local ancestry using continent specific variants) is a new method for ultra-fast and accurate inference of la in very large sequenced cohorts by using continent specific variants […]

library_books

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

2014
PLoS Comput Biol
PMCID: 3990492
PMID: 24743331
DOI: 10.1371/journal.pcbi.1003555

[…] as continent-specific variants (csvs) and model them within standard hidden markov models of local ancestry to achieve an accurate and computationally efficient method for local ancestry inference (lanc-csv). our model accounts for potential errors induced by low-coverage sequencing as well as by the finite sample size of the reference panels used for local ancestry inference. as opposed […]


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Lanc-CSV institution(s)
Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
Lanc-CSV funding source(s)
This work is supported in part by the National Institutes of Health (R03-CA162200, R01-GM053275 and T32-GM008185).

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