Issues installing vep

Question

[pmw]

I am having issues with installing ensembl's vep on the HPC. It requires perl dependencies which I have successfully installed most of via anaconda. However I get the following error message when trying to run perl INSTALL.pl:

Can't locate Module/Build.pm in @INC (you may need to install the Module::Build module) (@INC contains: ./Bio /rds/general/user/pmwells/home/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /rds/general/user/pmwells/home/anaconda3/lib/site_perl/5.26.2 /rds/general/user/pmwells/home/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /rds/general/user/pmwells/home/anaconda3/lib/5.26.2 .) at Build.PL line 20.

BEGIN failed--compilation aborted at Build.PL line 20.

ERROR: Shared Bio::DB:HTS library not found

I therefore tried manually installing perl DB HTS as follows - conda install -c bioconda perl-bio-db-hts but I still get the same error message during the next installation step (runnning INSTALL.pl). I would be very grateful for advice

Answer 1

[Juke34]

Why are you installing dependencies manually? Did you try conda install -c bioconda ensembl-vep ? It should install all dependencies for you.

[pmw]

Thank you, I wasn't aware of this option and so did it step by step. This is good to know though thank you!

I have now found variant recoder will work, however there doesn't seem to be an option to output rsIDs for the SNPs, which was my original reason for using the tool (I have them in chr:position... format).

[Emily]

You should get the rsID in your variant recoder output unless your variants are novel.

[pmw]

I don't get it unfortunately, the input SNPs are from UKBB Neale lab GWAS summary statistics.

I'm running:

./vep variant_recoder -i Cholesterol_GW_Sig_VEP_input.txt --grch37 --database

Do you know what may be going wrong?

I have an input whitespace delimited file in standard vep format

Thank you for your help

[Ram]

Why is this post an answer to your question? It looks like it is either a reply to Juke34's answer or a follow-up question. In either case, it should not be an answer. Please move this post (using the Drag/Drop hand icon - click and hold to drag and drop the post) to the appropriate location.

[Emily]

Can you give us a few lines of your input data, please?