Search Results for "snp map"
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Showing 6 open source projects for "snp map"
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A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data.
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GOBIG is a toolbox that can be used for detecting genetic variations. The project is intended to handle big data. What's more important is that it be used to detect clusters of SNP variants. It is the intention to use the toolbox with common and rare variants. To use it, for example, to find the genetic map of genes causing complex diseases.
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Lep-MAP
fast and accurate linkage map construction for large SNP datasets
Lep-MAP is a novel linkage map construction software. Note there is a new version, Lep-MAP2 available in https://sourceforge.net/projects/lepmap2/ Also note a bug in Lep-MAP: genotype alleles should be given in numerical order like "1 2", not as "2 1". If you use Lep-MAP, please cite Lep-MAP: fast and accurate linkage map construction for large SNP datasets Pasi Rastas; Lars Paulin; Ilkka Hanski; Rainer Lehtonen; Petri Auvinen Bioinformatics 2013; doi: 10.1093/bioinformatics... -
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mendelFix
Correction of SNP Mendelian errors in trio data
mendelFix is a Perl script for checking Mendelian errors in genome-wide SNP data of trio designs. The program takes 12-recoded PLINK PED and MAP files as input, and calculates a series of summary statistics for Mendelian errors, sets as missing offspring genotypes that present Mendelian inconsistencies, and implements a simplistic procedure to infer missing genotypes using parent information. The program can be easily incorporated in any pipeline for family-based SNP data analysis... -
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Bis-SNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Bis-SNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels...
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