[[TOC()]] = Coverage Analysis Pipeline = Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC = Coverage per base = [[Image(CoveragePerBase.png)]] '''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.