(2) germline
(3) fineSTRUCTRUE/paintingmychromosomes
(4) fastIBD/beagle
- BEAGLE's fastIBD method is described in
B L Browning and S R Browning (2011) A fast, powerful method for detecting identity by descent. The American Journal of Human Genetics 88:173-182. [
link to article ] - BEAGLE's methods for detecting homozygosity-by-descent and identity-by-descent are described in
S R Browning and B L Browning (2010) High-resolution detection of identity by descent in unrelated individuals. The American Journal of Human Genetics 86:526-539. [link to article]
- BEAGLE's methods for calling genotypes from genotype likelihood data are described in
B L Browning and Z Yu (2009) Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies. The American Journal of Human Genetics 85:847-861. [link to article]
- BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in
B L Browning and S R Browning (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223. [link to article]
- BEAGLE's methods for inferring haplotype phase or sporadic missing data in unrelated individuals are described in
S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet 81:1084-1097. [link to article]
- BEAGLE's methods for association testing are described in
B L Browning and S R Browning (2007)Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering .Genet Epidemiol 31:365-375. [link to article] BEAGLE's haplotype frequency model was first described in :S R Browning (2006) Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78:903-13. [link to article]
(5) Comparison of MCLUST with fineSTRUCTURE
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