Haplotype Creation Program

Question

[j.a.yearsley]

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

Answer 1

[Zev.Kronenberg]

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

[j.a.yearsley]

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?

[Zev.Kronenberg]

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