Haplotype Creation Program
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Entering edit mode
6.2 years ago
j.a.yearsley ▴ 10

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 • 1.8k views
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6.2 years ago

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

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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?

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

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