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We are experiencing failures with 32GB of RAM. Should we run with 64GB of RAM or do we have other options for controlling the amount of RAM used? (See below --buffer_size option)
The related line …
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Dear loftee
Im applying vep pluggin
singularity run --bind $PWD --pwd $PWD /programs/ensembl-vep-110.1/vep.sif vep --plugin LoFtool -i myinput.vcf -o myoutput --fork 8 -gff Homo_sapiens.GRCh38.10…
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Test_unit_module4_VEP.py only runs correctly when it is in the same directory as module4_VEP_code_only.py. I have leave it in the test folder for now...It only runs when it is placed in the same folde…
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Hi Brent,
I am wondering how I could keep certain vcf header values after using vcfanno for example:
##SnpEffVersion and ##SnpEffCmd
After using vcfanno to merge this vcf with a VEP(ed) vcf I…
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Hi,
I am running vcf2maf installed from conda. I skip VEP, since I prepared the VEP annotated VCF with sarek (https://nf-co.re/sarek/3.2.1/usage). Here the VEP version used is 108. The problem is …
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Hi,
I believe I have downloaded the files for hg38, but am unable to run LOFTEE with the below error. I've specified the LOFTEE_PATH, but it is still looking in /vep/loftee, and I do not have the…
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I successfully installed VEP in my ubuntu v.20 and added its path to `~/.bashrc` as shown below but still I get the error
`.bashrc` file content
```
export PATH="$PATH:/home/subudhak/ensembl-vep-re…
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Hello All,
First of all, thank you for implementing the variant recoder tool.
I have a very specific question about speeding up the variant recoder. I have ~21 million variants that I want to qu…
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$ perl vcf2maf.pl --input-vcf xxx.snp.vcf --output-maf test.maf --ref-fasta ../pig.dna.toplevel.fa
STATUS: Running VEP and writing to: xxx.snp.vep.vcf
ERROR: Cannot find VEP script under: /yyy/minic…