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Hi all, I'm testing the -T parameter in samtools pileup. According to the manual it should be the "error dependency coefficient in the maq consensus calling model". I've been googling around and seen that SOAPsnp also has a theta parameter. The only thing I've realized so far is that the higher the theta, the higher the snp score; it looks like snps are scored better if theta is high as if their "being different" from the reference is due to a real snp, whereas they are scored worse if theta is low as if their "being different" is due to an error in reading... Am I right? Can anybody explain this better? Also, is there a paper about this? Thanks d |
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The original maq paper had some supplemental methods that delved more into the math and statistics of different aspects of their algorithm. That may explain what the theta parameter/error dependency are designed to address, and how they function. Going to get that ASAP. Thanks
(24 Aug '10, 13:36)
dawe
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