<![CDATA[BOL: Manisha Mishra's blogs]]> https://bioinformaticsonline.com/blog/owner/manisha? https://bioinformaticsonline.com/blog/view/42188/tools-and-method-for-haplotype-phasing Fri, 04 Sep 2020 20:41:40 -0500 https://bioinformaticsonline.com/blog/view/42188/tools-and-method-for-haplotype-phasing <![CDATA[Tools and Method for Haplotype phasing !]]> Huge amounts of genotype data are being produced with recent technological advances, both from increasingly  comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods. The vast amount of knowledge contained in these results, however, is best  exploited through phased haplotypes, which classify the alleles co-located on the same chromosome. Since sequence and SNP array data normally take the form of unphased genotypes, one does not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele. Fortunately, new advances in both computational and laboratory methods promise improved determination of haplotype phase. Following are useful tools :
 

Arlequin: http://cmpg.unibe.ch/software/arlequin3/

BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html

fastPHASE: http://stephenslab.uchicago.edu/software.html

GENEHUNTER: http://linkage.rockefeller.edu/soft/gh/

The Genome Analysis Toolkit:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

IMPUTE2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

MACH: http://www.sph.umich.edu/csg/abecasis/MACH/

MERLIN: http://www.sph.umich.edu/csg/abecasis/Merlin/

PHASE: http://stephenslab.uchicago.edu/software.html

PL-EM: http://www.people.fas.harvard.edu/~junliu/plem/

“Read-backed phasing” algorithm: http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

SHAPE-IT: http://www.griv.org/shapeit/

]]> Manisha Mishra