Thursday, 14 April 2011

Want to use samtools for polyploid organisms?

Well the short answer is you can't.
Here's what Heng Li has to say
Samtools is designed for diploid genomes. I would recommend to treat a haploid genome as diploid and filtering heterozygotes afterwards. For higher ploidy (>2), samtools does not work well. For pooled resequencing, specialized SNP callers (such as syzygy and a few others) are better.

Other recommendations are

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Datanami, Woe be me