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Old 08-23-2012, 06:44 PM   #1
empyrean
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Location: EU

Join Date: Sep 2010
Posts: 52
Default Haplotype caller

hi..

I have 454 Amplicon sequencing data for a tetraploid potato crop. we have sequenced few genes of interest from several different genotypes. My aim is to seperate genotypes and sub genomes here. I am thinking of using haplotype analysis to seperate the genotypes as well as sub genomes here.

As i am new to this, can someone point me to some tools / softwares which can take the input i have and give haplotypes as output? All i have is gene sequences, and mapped bam file and raw reads. I dont have any marker data or genotype data with me.. i know they are sampled form 10 genotype of one type and other 5 are of other type..
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