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Old 04-11-2013, 06:24 PM   #6
Rainbird
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Location: US

Join Date: Dec 2012
Posts: 16
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Thanks Khen.
If I undertand correctly, samtools is designed for diploid genome. If there are 2 alleles in your sample other than the allele in the reference genome (for example, the reference genome has a T, and you have a A and a G in your sample), samtool might not work well.

Is there any tool specifically designed to find allele frequency in your own samples regardless what is in the reference genome?
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