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