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Old 12-10-2009, 03:11 AM   #1
Mr Mutundes
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Location: Sydney, Australia

Join Date: Jan 2009
Posts: 17
Default bwa - samtools - SNPs

Hi,

I am interested in hearing from anyone who has successfully used the combination of bwa and samtools to identify SNPs from paired SOLiD reads. Working with simulated reads at the moment I am getting nice alignments but my pileup output from samtools is pretty wacky... so I'd like to know if in anyone else's hands this can actually work.

Thanks
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