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