Question: Haplotype Creation Program
1
gravatar for j.a.yearsley
5.0 years ago by
j.a.yearsley10
European Union
j.a.yearsley10 wrote:

Hi,

I have got some NGS data and identified certain SNPs. I now want to create the two haplotypes for each individual. I have used freebayes to identify the SNPS but it does not create a haplotype. I used HapCompass also but even though this identified the SNPs onto the correct haplotype it only gave me the SNPS not the full haplotype. Is there a way I can use a reference sequence and then be able to overlay the SNPs so that I actually get the full haplotype or a program that will used a reference for me? Any help much appreciated! I'm relatively new to bioinformatics..

Thanks,

James

snp next-gen • 1.6k views
ADD COMMENTlink modified 5.0 years ago by Zev.Kronenberg11k • written 5.0 years ago by j.a.yearsley10
1
gravatar for Zev.Kronenberg
5.0 years ago by
United States
Zev.Kronenberg11k wrote:

You need a population to phase your samples.  If you have human data, download the 1kg calls and use them as a background for phasing.  I like using Beagle for phasing http://faculty.washington.edu/browning/beagle/beagle.html

ADD COMMENTlink written 5.0 years ago by Zev.Kronenberg11k

I've got 47 individuals from a population already sequenced and it's not human data. Ive already created a reference sequence out of them to compare against. would that work?

ADD REPLYlink written 5.0 years ago by j.a.yearsley10

We have used BEAGLE to phase 40 genomes with reasonable accuracy. 

ADD REPLYlink written 5.0 years ago by Zev.Kronenberg11k
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