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

II. Tools:

1. qaComputeComputes 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 underINT 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 considerthe entire span of the insert as a read, if insert size islower than INT.For an accurate estimation of span coverage, I recommendsetting an insert size limit INT around 3*std_dev of your lib'sinsert 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. removeUnmappedRemove unmapped and sub-par quality reads from a bam/sam file.For more info on the parameters try ./removeUnmapped

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