Differences
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strviper [2017/05/03 14:33] – mikael | strviper [2018/03/20 09:48] (current) – mikael | ||
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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. | 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. | ||
- | 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; | + | 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, |
- | === Installation === | + | === Installation |
- | 1. Download the strviper package. | + | 1. Download the strviper package: http:// |
2. Unzip the package to $PATH_TO_STRV (i.e., tar zxvf strviper.tar.gz) | 2. Unzip the package to $PATH_TO_STRV (i.e., tar zxvf strviper.tar.gz) | ||
3. Add $PATH_TO_STRV/ | 3. Add $PATH_TO_STRV/ | ||
- | === Making Variations Calls === | + | === Installation (JAPSA version) === |
+ | |||
+ | 1. Download JAPSA from https:// | ||
+ | 2. Follow instructions there | ||
+ | |||
+ | === Call variation (original version) | ||
Preprocessing: | Preprocessing: | ||
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$ 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 | ||