Calculates a minor allele frequency in (pooled) genomic sequencing.

Given a BAM file and a genomic reference, for each position covered in the
BAM file, show the reference base, the potential minor allele, and probable
background.

This assumes that if a SNP exists, there is likely only one possible variation.
So, this calculation will fail if more than one minor allele is present.  This
also ignores indels.

If R is installed and -alleles is given, this will also calculate a 95%
confidence interval. If rpy2 is installed, that bridge will be used to call R,
otherwise a process is forked for each allele.


Usage: bamutils minorallele {opts} in.bam ref.fa

Arguments:
  in.bam        BAM files to import
  ref.fa        Genomic reference sequence (indexed FASTA)

Options:
  -name    name  Sample name (default to filename)
  -qual    val   Minimum quality level to use in calculations
                 (numeric, Sanger scale) (default 0)
  -count   val   Only report bases with a minimum coverage of {val}
                 (default 0)
  -ci-low  val   Only report bases where the 95% CI low is greater than {val}
                 (default: show all)
  -alleles val   The number of alleles included in this sample
                 If given, a Clopper-Pearson style confidence interval will
                 be calculated. (requires rpy2 or R)

rpy2 not detected! Consider installing rpy2 for faster processing!