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| Both sides previous revision Previous revision Next revision | Previous revision | ||
| strviper [2017/05/03 14:31] – mikael | strviper [2018/03/20 09:48] (current) – mikael | ||
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| STRViper is written in Java and hence can be run cross platforms. We provided scripts for conveniently running STRViper on Unix, Linux and MacOS and scripts for Windows are under development. | STRViper is written in Java and hence can be run cross platforms. We provided scripts for conveniently running STRViper on Unix, Linux and MacOS and scripts for Windows are under development. | ||
| - | A manuscript describing STRViper is currently under review for submission. If you are interested in knowing more about STRViper, please contact Minh Duc Cao (minhduc.cao@gmail.com) for a copy of the manuscript. If you find STRViper useful for your research, please cite it in your publications. Contact Minh Duc Cao or revisit this page for a citation. | ||
| - | === Installation === | + | If you are interested in knowing more about STRViper, please contact Minh Duc Cao (minhduc.cao@gmail.com). If you find STRViper useful for your research, please cite it in your publications. |
| - | Download the strviper package. | + | Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S and Bodén M (2014) Inferring Short Tandem Repeat Variation from Paired-End Short Reads, //Nucleic Acids Research//. Feb;42(3):e16. DOI: [[http://dx.doi.org/10.1093/nar/ |
| - | Unzip the package to $PATH_TO_STRV | + | |
| - | Add $PATH_TO_STRV/scripts to you $PATH | + | |
| - | === Making Variations Calls === | + | === Installation (original version) === |
| + | |||
| + | 1. Download the strviper package: http:// | ||
| + | 2. Unzip the package to $PATH_TO_STRV (i.e., tar zxvf strviper.tar.gz) | ||
| + | 3. Add $PATH_TO_STRV/ | ||
| + | |||
| + | === Installation (JAPSA version) === | ||
| + | |||
| + | 1. Download JAPSA from https:// | ||
| + | 2. Follow instructions there | ||
| + | |||
| + | === Call variation (original version) | ||
| Preprocessing: | Preprocessing: | ||
| Line 47: | Line 55: | ||
| $ jsat.str strv2vcf --input lib.strv --output lib.vcf --reference TAIR10.fas | $ jsat.str strv2vcf --input lib.strv --output lib.vcf --reference TAIR10.fas | ||
| + | |||
| + | === Call variation (JAPSA version) === | ||
| + | |||
| + | As above but note the equivalent programs are in: | ||
| + | |||
| + | jsa.trv.parseTRF | ||
| + | jsa.trv.sam2fragment | ||
| + | jsa.trv.sortFragment | ||
| + | jsa.trv.fragment2var | ||