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michy · 12-09-2009, 08:41 AM

Hello,
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

12-09-2009, 08:41 AM	#1
michy Junior Member Location: oxford Join Date: Aug 2008 Posts: 5	MAQ and SNP calling Hello, 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