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Old 12-09-2009, 08:41 AM   #1
michy
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Default 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
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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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Old 12-10-2009, 02:21 AM   #3
bioenvisage
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can any one tell me the details regarding the alignment output of maq

Last edited by bioenvisage; 12-10-2009 at 02:35 AM.
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Old 12-11-2009, 09:23 AM   #4
BertieWooster
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can any one tell me the details regarding the alignment output of maq


Well, the maq map output itself is binary. You can run the pileup command to give you the read bases and the quality at each position. Check the maq documentation and that should elaborate further what the columns in the output are.

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