Interval file

The interval file (or bed file) is a mandatory input for VisCap. It has to be the exact same interval file that was use for running the depthOfCoverage tool. This interval file format should be the following:

1. It has to be a tab separated file, with minimum four columns: chromosome, start, end, interval name.
2. It may or may not have a header. If you include a header, comment out the header line with '#'.
3. An example of an interval file is the following.

#chrom   start   end   interval_name
chr1    12918859        12919156        PRAMEF2
chr1    12919542        12920131        PRAMEF2
chr1    12921070        12921639        PRAMEF2
chr1    16174557        16174650        SPEN,FLJ37453
chr1    16199305        16199636        SPEN
chr1    16200604        16200895        SPEN
chr1    16202691        16203178        SPEN
chr1    16235810        16235981        SPEN
chr1    16237590        16237801        SPEN
chr1    16242617        16242779        SPEN
chr1    16245415        16245551        SPEN
chr1    16245893        16246017        SPEN