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CNV Annotation of Segmentation Files For Canine

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

cnv canfam4 annotation
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written by josh.mannheimer • josh.mannheimer

1 answer

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

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written by colindaven colindaven

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

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written by josh.mannheimer • josh.mannheimer

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