CNV Annotation of Segmentation Files For Canine

Question

[josh.mannheimer]

Hi all,

I have several copy number segmentation files that have been aligned to CanFam4 (canine). I just need to match the chromosomal coordinates on the segmentation files with the corresponding gene annotations. I know there is software for humans that is capable of this but I have not found any dog. In the event that no software is available I am guessing I would have to match the coordinates to the gtf using a custom script, is there a straightforward was this can be done. Thanks

Answer 1

[colindaven]

Is there any reason you can't just convert both files to bed format, then use bedtools intersect ?

[josh.mannheimer]

I am not familiar with using bed files but will look into this. Thank you for your suggestion.