A couple of useful qa tools for sequencing data.

I. Setup:

Use make SAMTOOLS=/PATH/TO/SAMTOOLS/SOURCE VERSION=SAMTOOLS_VERSION If you don't have samtools, download it from here (and run make): http://samtools.sourceforge.net Any version should work. However, 1.3 is verified to do such.

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 .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