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Old 06-09-2010, 04:09 PM   #1
cggj
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Location: Houston

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Default Data issues...

Hi all,

I am working with some exome sequencing data. I have done the mapping, pileup, filtering and variant calling. After all that... my data look weird, I am getting A LOT of homozygous calls and when annotating most of them are not in dbSNP. These things make me suspicious about my data. Also, I checked a few of the heterozygous SNPs and 1/10 was actually heterozygous.
Does anyone have any idea of what might be wrong with my data??? Is there a way to check if the sequencing actually worked, besides relying on the Phred-like scores???

Thank you!
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Old 06-09-2010, 07:00 PM   #2
john_mu
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One sanity check is to see what % of your reads mapped to the genome. If that is very low (like less than 10%), something could be wrong.
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