# HG changeset patch
# User geert-vandeweyer
# Date 1411718242 14400
# Node ID b9647583dbea725e9c4feb32608851dd2c323e20
# Parent  8cfdb91bfc14416f1cbe82853c83134b9b9956fb
Uploaded

diff -r 8cfdb91bfc14 -r b9647583dbea readme.rst
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+++ b/readme.rst	Fri Sep 26 03:57:22 2014 -0400
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+BACKGROUND:
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+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. 
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+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). 
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+LIMITATION:
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+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.
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+Any feedback is welcome
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+
+INSTALLATION:
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+After installation, complete the dbsnp.loc and dc_genotyper_indexes.loc files. The DC_genotyper_indexes.loc file has a specific format, specifying two index files per genome in a single line. Make sure you use comma to seperate these. DCG supports multithreading, but keep tests have shown that using more than 6-8 threads will lead to I/O bottlenecks.