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