Merge branch 'master' of git.embl.de:rmuench/metaSNP

README.md

@@ -73,7 +73,7 @@ Workflow:
 =========
 **__Note:__ Each part is dependened on the successful completion of the previous one.**
 
-## 1. Initiate a NewProject with NewProject.sh
+## 1. Initiate a new project
 
         usage: ./NewProject.sh project_dir
     
@@ -131,9 +131,9 @@ Note: requires SNP calling (Part II) to be done!
 Example Tutorial
 ================
 
-## 1. Run the setup & compilation steps and acquire the provided reference database.
+## 1. Run the setup & compilation steps and download the provided reference database.
 
-## 2. Go to the EXAMPLE directory and acquire the samples with the getSamplesScript.sh
+## 2. Go to the EXAMPLE directory and download the samples with the getSamplesScript.sh
 
     $ cd EXAMPLE
     $ ./getSamplesScript.sh
@@ -151,7 +151,7 @@ Example Tutorial
     $ ./createCovComputationRun.sh tutorial/ tutorial/all_samples > runCoverage
     $ bash runCoverage
 
-## 6. Perform the work load balancing for parallelization into five jobs.
+## 6. Perform a work load balancing step for run time optimization.
 
     $ ./createOptSplit tutorial/ db/Genomev9_definitions 5
     $ bash runCoverage
@@ -162,11 +162,13 @@ Example Tutorial
     $ bash runSNPcall
 
 ## 8. Run the post processing / filtering steps
-Compute allele frequencies for each position that pass the given thresholds.
+### a) Compute allele frequencies for each position that pass the given thresholds.
 
     $ ./filtering.py tutorial/tutorial.all_perc.tab tutorial/tutorial.all_cov.tab tutorial/snpCaller/called_SNPs.best_split_* tutorial/all_samples tutorial/filtered/pop/
 
-
+### b) Compute pair-wise distances between samples on their SNP profiles and create a PCoA plot.
+    
+    TODO!
 
 Basic usage
 ===========
@@ -177,7 +179,7 @@ You will find scripts as well as the binaries for qaCompute and the metaSNP call
 Additional information and options (tools and scripts):
 ---------------------------------------------------------
 
-###metaSNP caller
+### metaSNP caller
 Calls SNPs from samtools pileup format and generates two outputs:
 
         usage: ./snpCall [options] < stdin.mpileup > std.out.popSNPs
@@ -197,7 +199,7 @@ Population wide variants that occur with a frequency of 1 % at positions with at
 Non population variants, that occur with a frequency of 10 % at positions with at least 10x coverage.
 
 
-###[qaComput](https://github.com/CosteaPaul/qaTools)
+### [qaComput](https://github.com/CosteaPaul/qaTools)
 Computes normal and span coverage from a bam/sam file. 
 Also counts unmapped and sub-par quality reads.
 
@@ -236,7 +238,7 @@ Also counts unmapped and sub-par quality reads.
    For more info on the parameteres try ./qaCompute
    
 
-###filtering.py
+### filtering.py
    
 usage: metaSNP filtering [-h] [-p PERC] [-c COV] [-m MINSAMPLES] [-s SNPC]
                          [-i SNPI]