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Old 04-26-2010, 08:47 AM   #1
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Location: barcelona

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Default PEM data: edit distance

I'm trying to use VariationHunter to detect SVs based on PEM data generated by Illumina tech.
One of the parameters required as input for the program is theedit distance per mapped pair, and I have no clue about the meaning of this param. In the examples of the usage file it appears as an integer value ranging from 0 to 4.
Any idea???

Thanks a lot
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Old 07-04-2010, 09:57 AM   #2
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Location: LA

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Default PEM data: edit distance

As per my knowledge it is 2bp for 36bp read length, 3bp for 50bp read length and 4 bp for 75 bp read length.

But I am not very sure. I replied cause no one else did.

Though I have a question how do you calculate the Avgphred and ProbBased Phred ?
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