Coverage Analysis Pipeline

Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC

Coverage per base

Description: Calculates coverage per base. Creates a text file which you can use to make a histogram (coverage versus frequency)

Input:

• SortedBamFile, a sorted bam file
• ChromSizesTxt, e.g. the chromInfo.txt from the UCSC database

Output:

• coverageHistogram: summary of coveragePerBase. An overview about the genome coverage of the sequence experiment. Load this into excel/calc/gnuplot/some-other-program to make a graph

Requirements:

• BEDtools - ​http://code.google.com/p/bedtools/ (v2.9.0 and probably later versions)

Status: Implemented on grid. Source code is made available.