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Old 03-31-2011, 04:05 AM   #2
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Location: Germany

Join Date: Oct 2008
Posts: 415

I would use Samtools as it is under active development and Maq, to my knowledge, is not any more.

However for SNP calling try the mpileup pipeline described on the Samtools webpage instead of using pileup. It's important to generate the I16 info fields for variant calling in our experience.
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