Merge branch 'master' of lsource2.decode.is:stat/popSTR

Author: Snaedis Kristmundsdottir

README.md

@@ -1,5 +1,7 @@
 # PopSTR - A Population based microsatellite genotyper
 
+Pre-step: Install dependencies (if not present) `deps.sh`
+
 ## Downloading release with static binary
 
 1.Download static binary https://github.com/DecodeGenetics/popSTR/releases/download/2.0/popSTR and zip of source code https://github.com/DecodeGenetics/popSTR/archive/2.0.zip
@@ -20,7 +22,9 @@
 
 4.Run install script `install.sh`
 
-5.[Optional] To make sure installation succeeded, execute runSmall.sh with a bamList(described below) and path to reference: `runSmall.sh bamList reference`
+5.Run setup script: `setUp.sh`
+
+6.[Optional] To make sure installation succeeded, execute runSmall.sh with a bamList(described below) and path to reference: `runSmall.sh bamList reference`
 This will genotype the samples in `bamList` over a set of markers from chr21 and write the results to `./vcfs/chr21_small_0.vcf`. Two other files `pnSlippage` and `markerSlippageChr21_0` are also generated. `pnSlippage` contains slippage rates for all samples in `bamList` and `markerSlippageChr21_0` contains slippage and stutter rates for the genotyped markers.
 
 ## Running popSTR