Tools

Some tools that I wrote.

pileupcvg.c

Take as input a bam file and a chromosome id and outputs the coverage at each nucleotide position in the chromosome.

resample.c

Reads a table from standard input and resamples it into bins.

average.py

Reads table from standard input and calculates average (mean, median or mode)

bambaseatpos.c

Prints in SAM format those alignments from a BAM file which contain a given base (or indel) at a given reference position