Finding overlap between BAM files or BAM and gff3 files

Question

[Pappu]

I want to find the overlap and display it nicely. I am am wondering which tool will be suitable for it.

[ivivek_ngs]

Yes @igor is correct, the question needs to be modified or much detailed clarification is needed. What is your area of interest that you want to see by intersecting the bam files. If you merely wants to see how the reads are piled up for both the bams you can just create a .tdf file for each of them and display in IGV as highlighted above. Alternatively to give it more precision you would need to calculate the overlapping features for your ROI (region of interest) then you can take a look at the bedtools (highlighted in @igor answer) or bedops. Converting your bam files to bed files and then trying to intersect the two bed files for the ROI and then highlighting those regions in IGV once you have uploaded the *.tdf files in the IGV browser. Not necessarily you need to convert things to bed , bedtools handles bam as well. Only thing to keep in mind is to what kind of bam files are they? are they RNA-Seq or ChIP-Seq or Whole exome bams or Whole genome bams? Answers will be tweaked according to that. In any case if you want to compare visually you can take a look at deeptools as well. bamCompare or bamCorrelation is what you might be interested.

Answer 1

[igor]

You should clarify the question. It can be interpreted in multiple ways.

If you want to display BAM or GFF files nicely, I would suggest IGV. You can load them in there and they will be displayed and you can adjust sizes and colors.

If you want to compare them more programmatically, BEDTools (and a few similar alternatives) offers that. Many of the tools in the suite work with not just BED, but also BAM/GFF/VCF files. It sounds like what you are looking for is bedtools intersect: