Mercurial > repos > geert-vandeweyer > dc_genotyper
changeset 8:b9647583dbea draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Fri, 26 Sep 2014 03:57:22 -0400 |
| parents | 8cfdb91bfc14 |
| children | 7cbbf8aaa46c |
| files | readme.rst |
| diffstat | 1 files changed, 18 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Sep 26 03:57:22 2014 -0400 @@ -0,0 +1,18 @@ +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.