Aziz Khan
Aziz Khan
I was getting the same error `Unknown option: af_gnomad`. But when tried with `VEP version 103.1`, it worked.
Apologies for the late response. The current version doesn't have an option to set the max and min scale. It uses the min and max from the pairwise matrix.
When you intersect with intervene the order of your files does matter and you will end up having slightly different results with a different order. Also, make sure that for...
Thanks @Rohit-Satyam for your interest and input. @amizeranschi `Intervene` is not designed to give you a list of overlapping regions, rather it spits out how many of the individual regions...
Hi @dllahr you're using an old version `v0.5.8` of the tool. Please try to install the latest version `0.6.5` using: `conda install intervene=0.6.5 -c bioconda` or `pip install intervene==0.6.5`
@dllahr It seems is using the python 2.7., or potentially you conda `base env` has python 2.7. Can you please try this? `conda create -n intervene3 python=3.6 intervene=0.6.5 -c bioconda`
Please check this issue https://github.com/asntech/intervene/issues/27
You should use like this: `intervene venn -i *.bed --bedtools-option s` instead of `s=True` or `-s`
Hi @hdingwall can you please try to install it using pip, which worked for @Phillip-a-richmond. I'll look into this issue soon. Thanks!
Hi @scalavision, yes it is pybedtools which creates temp files. Are you still getting this error? I'm looking into this.