strviper

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strviper [2018/03/20 09:19] – mikaelstrviper [2018/03/20 09:48] (current) – mikael
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 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/gkt1313|10.1093/nar/gkt1313]]. 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/gkt1313|10.1093/nar/gkt1313]].
  
-=== Installation ===+=== Installation (original version) ===
  
   1. Download the strviper package: http://bioinf.scmb.uq.edu.au:8080/STRViper/strviper.tar.gz   1. Download the strviper package: http://bioinf.scmb.uq.edu.au:8080/STRViper/strviper.tar.gz
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   3. Add $PATH_TO_STRV/scripts to you $PATH   3. Add $PATH_TO_STRV/scripts to you $PATH
  
-=== Making Variations Calls ===+=== Installation (JAPSA version) === 
 + 
 +  1. Download JAPSA from https://github.com/mdcao/japsa 
 +  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
  
  • strviper.1521497996.txt.gz
  • Last modified: 2018/03/20 09:19
  • by mikael