Haplotype calls from Amplicon Sequencing

[empyrean]

Hi.. i have data for two groups.. one group has 10 diffent strains and other group has 5 different strains. 40 genes are selected and primers are designed for these genes. Sequencing is performed on these amplicons which has length of around 300bp. Now i need to identify haplotypes by mapping them to the reference genes. I have to identify haplotypes for each strain as well across the strains. The data i have is reference genes and 454 reads. How to proceed please suggest me.

I mapped the reads using bwa-sw and called the SNPS. This is not working. Tried to use Haploview, hapcut, etc.. but they have their own diff way of input needed like haploview takes input from hapmap project like that.. is there any tool which maps these reads and give haplotypes as output?

[JackieBadger]

http://seqanswers.com/forums/showthread.php?t=18055

[empyrean]

thankyou for the reply.
jhmc is asking for pcr primers as tags. but i dont know the pcr primers. Also i dont see it constructing a haplotype map. all i have is sequencing reads and reference genes file.

[JackieBadger]

you want to create a haplotype map? Do you mean a minimum spanning or median-joining network network?
As i mentioned before, there is much more to take into consideration. You can not accept sequences as true variants from a reference on the merit of their existence. You need to take into consideration replication, bp mismatch errors, and possibly chimeric sequences.

If I understand what you want to do, SESAME can do this