Suppose I have a bam file that contains mapping of reads to the human reference. Then for a particular gene, I want to reconstruct its two haplotypes. Is there a tool to assemble reads mapped to the said gene region into two haplotypes? Thanks!
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You can extract reads from a given region from your sam/bam file. about assembling it ... u should be assemble it into a gene but about getting two haplotypes i can't say because then you would need to assess the variants in the region and then mix and match to get the 2 haplotypes but i doubt that'll be of much use or of any significance.Originally posted by ymc View Post -
Check out the software wiki and/or try a Google search of "haplotype from short-read sequencing".Comment
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Thank you for your hint. I think I am going to implement the dynamic programming algorithm described in He et al (2010) and give it a try. I want to assemble only several hundred bases long exons. I think DP should be ok for my problem.Originally posted by HESmith View PostComment
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