Mercurial > repos > geert-vandeweyer > dc_genotyper
diff readme.rst @ 0:e8a32d824f39 draft
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author | geert-vandeweyer |
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date | Thu, 25 Sep 2014 05:24:35 -0400 |
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children | 15be98f10c13 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Thu Sep 25 05:24:35 2014 -0400 @@ -0,0 +1,13 @@ +BACKGROUND: + +DC_Genotyper stands for Deep-Coverage Genotyper, and is aimed at detecting low fraction SNPs (no indels) in high-ploidy (or pooled) samples with very high coverage. It is being developed at the University of Antwerp by Geert Vandeweyer. + +METHOD: + +DC_Genotyper generates a background noise distributions on a per-sample basis, and uses these distrubutions to detect non-reference sites. For non-reference sites, Allele-specific distributions are used to estimate if an allele surpasses the background signal (e.g. A_to_G has different distribution as A_to_C, also reflected in Tr/Tv ratios). + +LIMITATION: + +This is a very early version with several limitations. Current limitations are : no support for indels, no plotting of the noise-models, incorrect syntax in for multi-allelic sites in the VCF file. + +Any feedback is welcome