gravatar for FL512

2 hours ago by

I am thinking about how I can extract shared overlap interval from WGS data with arbitrary percentage.

According to the bedtools document, overlapping intervals can be extracted.
bedtools.readthedocs.io/en/latest/content/tools/intersect.html
This is very useful and working well for me if I have a few samples.

However, I am analyzing several hundreds of samples, ended in no overlapped interval detected.
This is understandable, let's say if 99 samples have T/A variant on the Chr1 position 1 but 1 sample does not have it, it results in no shared overlap interval.
To overcome this situation, I would liked to extract variants that are overlapped in more than 99% among samples, 95%, 90% or even less, until I can find the overlapping intervals.

Does anyone know how to do it or could you please let me know the helpful websites?
Or maybe GATK SelectVariants is doable?

Thank you!



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