Mercurial > repos > geert-vandeweyer > dc_genotyper
comparison readme.rst @ 8:b9647583dbea draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Fri, 26 Sep 2014 03:57:22 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 7:8cfdb91bfc14 | 8:b9647583dbea |
|---|---|
| 1 BACKGROUND: | |
| 2 | |
| 3 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. | |
| 4 | |
| 5 METHOD: | |
| 6 | |
| 7 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). | |
| 8 | |
| 9 LIMITATION: | |
| 10 | |
| 11 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. | |
| 12 | |
| 13 Any feedback is welcome | |
| 14 | |
| 15 | |
| 16 INSTALLATION: | |
| 17 | |
| 18 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. |