Igor Pozdnyakov

After installing VEP (https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html) there's no `/my_user_dir/vep` directory . There is however` /my_user_dir/ensemble-vep` which contains `ensembl-vep/examples/homo_sapiens_GRCh37.vcf `file (alogn with other samples). Trying to use the path to that file with...

UPDATE: I downloaded two files from Broad Institute website that the script complained about and placed them into locations where the script is looking for them: `/my_user_dir/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz` `/my_user_dir/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz` The error...

Just executed these: ``` export VCF2MAF_URL=`curl -sL https://api.github.com/repos/mskcc/vcf2maf/releases | grep -m1 tarball_url | cut -d\" -f4` curl -L -o mskcc-vcf2maf.tar.gz $VCF2MAF_URL; tar -zxf mskcc-vcf2maf.tar.gz; cd mskcc-vcf2maf-* perl vcf2maf.pl --man perl...

Hi again Cyriac, That gist also mentions apt-get / yum command that can't be executed on a Mac, but that does not matter now. After I point to the .fa...

Thanks, I think I got through all the VEP installation steps in https://gist.github.com/ckandoth/5390e3ae4ecf182fa92f6318cfa9fa97 successfully, besides the final test. Just couple of minor points, probably only #4 needs to be resolved:...

I installed Bio::DB::HTS using cpan so the error about tabix is gone. However, it did not help with the test, same error about SIFT missing. Sorry but google is not...

Hi, thanks for checking. Yes, it's the same error but I did not change anything since then.. Should I try to upgrade something?