Question: Reconstruct Alternative Haplotypes From Short Reads?
5
gravatar for Ahdf-Lell-Kocks
6.2 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

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?

short haplotype reference • 2.0k views
ADD COMMENTlink written 6.2 years ago by Ahdf-Lell-Kocks1.6k
4
gravatar for Brad Chapman
6.2 years ago by
Brad Chapman9.2k
Boston, MA
Brad Chapman9.2k wrote:

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

ADD COMMENTlink modified 3.4 years ago by Leonor Palmeira3.6k • written 6.2 years ago by Brad Chapman9.2k
1
gravatar for 2184687-1231-83-
6.1 years ago by
2184687-1231-83-4.9k wrote:

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

ADD COMMENTlink written 6.1 years ago by 2184687-1231-83-4.9k
0
gravatar for Zev.Kronenberg
6.1 years ago by
United States
Zev.Kronenberg11k wrote:

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

ADD COMMENTlink written 6.1 years ago by Zev.Kronenberg11k
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