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Old 12-09-2009, 08:41 AM   #1
Junior Member
Location: oxford

Join Date: Aug 2008
Posts: 5
Default MAQ and SNP calling

I've used MAQ to call SNPs in Illumina data, it worked fine apart from the read depth. When I looked at the alignment using IGV the read depth is often alot more. Im sure theres a reason, can anyone tell me why?.

Thank you
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