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Old 01-29-2014, 07:18 PM   #15
Location: Russia, Novosibirsk

Join Date: Oct 2013
Posts: 13

I had the same problem. I think the problen is that bcftools works with bcf-file but you don't specify for samtools to output bcf. So you should add to samtools mpileup command argument -g.

Hope this was helpful.
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