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Old 12-09-2009, 04:48 PM   #2
nilshomer
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Quote:
Originally Posted by michy View Post
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
Look at the default filtering: mapping quality etc. These may be reducing coverage (filtering reads) during SNP calling. This is a good thing, since poorly mapped reads or high-error reads may introduce artifacts.
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