[Bio-software] problem with polybayes

greigite via bio-soft%40net.bio.net (by sherisim from gmail.com)
Mon Oct 23 16:12:12 EST 2006


I'm trying to implement PolyBayes for SNP detection in a large
metagenomic dataset, using the *ace file from phredPhrap/Consed as
input. The problem I'm having is that PolyBayes only seems to find SNPs
in clones for one strand, but not the other one. This means that I'm
missing sometimes more than half the SNPs, as regions of high coverage
have many clones going in both directions. Are there any parameter
changes in consed or PolyBayes I can make that will allow me to detect
all SNPs?

Thanks for any advice,
Sheri



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