Some tools that I wrote.
Take as input a bam file and a chromosome id and outputs the coverage at each nucleotide position in the chromosome.
Reads a table from standard input and resamples it into bins.
Reads table from standard input and calculates average (mean, median or mode)
Like average.py but can return different statistics according to a format string
Prints in SAM format those alignments from a BAM file which contain a given base (or indel) at a given reference position