view readme.rst @ 20:8262299f8f3c draft

Fixed loading of dbsnp after bcftools-tabix switch.

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


INSTALLATION:

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.