Commit ed95c0bc authored by Robin Erich Muench's avatar Robin Erich Muench
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Update README.md

parent b85b8f82
......@@ -71,8 +71,6 @@ Note: Replace '/path/2' with the corresponding global path.
Workflow:
=========
**__Note:__ Each part is dependened on the successful completion of the previous one.**
## Required Files:
* **'all\_samples'** = a list of all BAM files, one /path/2/sample.bam per line (avoid duplicates!)
* **'ref_db'** = the reference database in fasta format (f.i. multi-sequence fasta)
......@@ -86,7 +84,8 @@ Workflow:
Generates a structured results directory for your project.
## 2. Part I: Pre-processing [optional]
Note: This part can be skipped if you do not want to balance the workload or you already performed the pre-processing for this dataset (samples).
Note: Subsequent SNP filtering depends on these coverage estimations.
This part can be skipped if you only want to use the 'raw' SNP output and do not intend to balance the workload or if you already performed the pre-processing for the dataset.
### a) run metaSNP_COV
......@@ -209,16 +208,13 @@ Example Tutorial
TODO!
Basic usage
===========
Basic usage (tools and scripts)
===============================
If you are interested in using the pipeline in a more manual way (for example the metaSNP caller stand alone) feel free to explore the src/ directory.
You will find scripts as well as the binaries for qaCompute and the metaSNP caller in their corresponding directories (src/qaCompute and src/snpCaller) post compilation.
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
......@@ -230,7 +226,7 @@ Calls SNPs from samtools pileup format and generates two outputs.
Note: Expecting samtools mpileup as standard input
#### __Output__
### __Output__
1. Population SNPs (pSNPs):
Population wide variants that occur with a frequency of 1 % at positions with at least 4x coverage.
......@@ -238,11 +234,12 @@ 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.
#### __Parameters:__
### __Parameters:__
m - Compute median coverage for each contig/chromosome.
Will make running a bit slower. Off by default.
......@@ -277,8 +274,8 @@ Also counts unmapped and sub-par quality reads.
For more info on the parameteres try ./qaCompute
### filtering.py
metaSNP_filtering.py
--------------------
usage: metaSNP filtering [-h] [-p PERC] [-c COV] [-m MINSAMPLES] [-s SNPC]
[-i SNPI]
perc_FILE cov_FILE snp_FILE [snp_FILE ...]
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