Reconstruct Alternative Haplotypes From Short Reads?

Question

[Ahdf-Lell-Kocks]

Are there any tools to reconstruct alternative haplotypes to the genome reference from short read sequencing data? For example, if one has prior knowledge that there might be duplicated or diverged haplotypes for gene X in the resequencing of a human individual, what tools can be used to reconstruct the putative alternative haplotypes in that gene X?

Answer 1

[Brad Chapman]

It sounds like you are looking for haplotype phasing. GATK has a short read phasing walker that works given an input VCF file of variants and the alignment reads in BAM format:

http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_phasing_ReadBackedPhasing.php

There are also more inference based methods. Wikipedia has a good treatment with links to several other packages:

http://en.wikipedia.org/wiki/Haplotype#Haplotype_resolution

Answer 2

[2184687-1231-83-]

Fermi claims to be able to reconstruct the different haplotype by preserving heterozygotes which are often collapsed by other assemblers: http://github.com/lh3/fermi/blob/master/README

Answer 3

[Zev.Kronenberg]

BEAGLE by Browning et al. It is super fast and can be used with the GERMLINE tool to look at haplotype and IBD.