Hello,

I have three CSV files of genomic intervals (chromosome start, stop, plus
other information in different columns) each containing between 10k-20k
lines.

I am looking for a way to pull out from one file only the lines that have
genomic overlap with both of the other two files. In other words, subset
file A to include only the lines of file A whose interval overlaps
intervals in Files B and C.

I'm able to create GRanges and manipulate these to get the subsetted
GRanges list, but I have not found a way to then use this GRanges as an
index to pull out the proper lines from CSV file.

Is there a simple way to subset my file in this way that I'm missing?

Thanks,
Giovanni

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