Commit a5209814 authored by Robin Erich Muench's avatar Robin Erich Muench
Browse files

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

parents f573c72a 1e08888c
...@@ -73,7 +73,7 @@ Workflow: ...@@ -73,7 +73,7 @@ Workflow:
========= =========
**__Note:__ Each part is dependened on the successful completion of the previous one.** **__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 usage: ./NewProject.sh project_dir
...@@ -131,9 +131,9 @@ Note: requires SNP calling (Part II) to be done! ...@@ -131,9 +131,9 @@ Note: requires SNP calling (Part II) to be done!
Example Tutorial 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 $ cd EXAMPLE
$ ./getSamplesScript.sh $ ./getSamplesScript.sh
...@@ -151,7 +151,7 @@ Example Tutorial ...@@ -151,7 +151,7 @@ Example Tutorial
$ ./createCovComputationRun.sh tutorial/ tutorial/all_samples > runCoverage $ ./createCovComputationRun.sh tutorial/ tutorial/all_samples > runCoverage
$ bash 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 $ ./createOptSplit tutorial/ db/Genomev9_definitions 5
$ bash runCoverage $ bash runCoverage
...@@ -162,11 +162,13 @@ Example Tutorial ...@@ -162,11 +162,13 @@ Example Tutorial
$ bash runSNPcall $ bash runSNPcall
## 8. Run the post processing / filtering steps ## 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/ $ ./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 Basic usage
=========== ===========
...@@ -177,7 +179,7 @@ You will find scripts as well as the binaries for qaCompute and the metaSNP call ...@@ -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): Additional information and options (tools and scripts):
--------------------------------------------------------- ---------------------------------------------------------
###metaSNP caller ### metaSNP caller
Calls SNPs from samtools pileup format and generates two outputs: Calls SNPs from samtools pileup format and generates two outputs:
usage: ./snpCall [options] < stdin.mpileup > std.out.popSNPs 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 ...@@ -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. 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. Computes normal and span coverage from a bam/sam file.
Also counts unmapped and sub-par quality reads. Also counts unmapped and sub-par quality reads.
...@@ -236,7 +238,7 @@ 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 For more info on the parameteres try ./qaCompute
###filtering.py ### filtering.py
usage: metaSNP filtering [-h] [-p PERC] [-c COV] [-m MINSAMPLES] [-s SNPC] usage: metaSNP filtering [-h] [-p PERC] [-c COV] [-m MINSAMPLES] [-s SNPC]
[-i SNPI] [-i SNPI]
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