University of Michigan Center for Statistical 
Genetics
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Yun Li's Software

The following software packages can be downloaded freely. If you find them useful, please email me: yunli@med.unc.edu. Comments and suggestions are welcome!

Concordance between two sets of genotype data (wiki) (source)
Concatenate Two Sets of Haplotypes
Dosage r2 Calculator
Extract information for a subset of sites from imputed dataset
LD Calculator from Phased Haplotypes (wiki)

KARMA

K-tuple Alignment with Rapid Matching Algorithm
Ligate Haplotypes with Overlapping

MaCH

MArkov Chain Haplotyping: rapid haplotyping, genotype imputation from genotype or resequence data (wiki)

MaCH-Admix

MArkov Chain Haplotyping for Admixed Populations

mach2dat

Imputation-based analysis of binary traits (windows version)
Imputation-based analysis of quantitative traits

prob2plink

Converts MaCH prob+info output to PLINK dosage file

r2_hat

Calculate Imputation Quality Estimate (r2_hat) from dosage data
Extract a Candidate Region from HapMap phase 1+2 for MaCH imputation

splitPed

Splits a pedigree file into smaller files with subsets of markers (wiki)

splitRef

Splits a reference haplotype file into smaller files with subsets of markers (wiki)

thunder

LD-based genotype caller and haplotyper on massively parallel sequencing data (wiki)
Weighted Haplotype and Imputation dosage Tests for multiple rare variants

Other

Filter a file by exactly matching key word in the first column
Imputation-based analysis of binary traits for family data without covariates
LD and Frequency Calculator

 
 

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