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README

A couple of useful qa tools for sequencing data.

I. Setup:

   Change Makefile $SAMTOOLS path to your samtools instalation path.
   If you don't have samtools, you can find it here:
      http://samtools.sourceforge.net/
   or
      git clone git://github.com/samtools/samtools.git
      cd samtools
      make

   Change $HTSLIB to installation path of htslib.
   If you don't have it, you can get it like this:
      git clone https://github.com/samtools/htslib.git 
      cd htslib
      make

   Just run make and you should be done!

II. Tools:

1. qaCompute
   Computes normal and span coverage from a bam/sam file.
   Also counts unmapped and sub-par quality reads.
   Parameters:
   m	    -	Compute median coverage for each contig/chromosome. 
   		Will make running a bit slower. Off by default.
   
   q [INT]  -   Quality threshold. Any read with a mapping quality under
                INT will be ignored when computing the coverage.
                
		NOTE: bwa outputs mapping quality 0 for reads that map with
		equal quality in multiple places. If you want to condier this,
		set q to 0.
   
   d        -   Print coverage histrogram over each individual contig/chromosome.
   	        These details will be printed in file <output>.detail
  
   p [INT]  -   Print coverage profile to bed file, averaged over given window size.  
   
   i        -   Silent run. Will not print running info to stdout.

   s [INT]  -   Compute span coverage. (Use for mate pair libs)
                Instead of actual read coverage, using the options will consider
                the entire span of the insert as a read, if insert size is
		lower than INT. 
 		For an accurate estimation of span coverage, I recommend
		setting an insert size limit INT around 3*std_dev of your lib's 
		insert size distribution.

   c [INT]  -   Maximum X coverage to consider in histogram.

   h [STR]  -   Use different header. 
                Because mappers sometimes break the headers or simply don't output them, 
		this is provieded as a non-kosher way around it. Use with care!

   For more info on the parameteres try ./qaCompute

2. removeUnmapped
   Remove unmapped and sub-par quality reads from a bam/sam file.
   For more info on the parameters try ./removeUnmapped

3. computeInsertSizeHistogram
   Compute the insert size distribution from a bam/sam file.
   For more info on the parameters try ./computeInsertSizeHistogram 

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