如何在 conda 中运行 ensembl-vep

Question

我是这样安装的：

conda install ensembl-vep=105.0-0

然后像这样安装人工缓存：

vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep —CONVERT

但我无法使用任何命令将其设置为运行，例如

vep --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105.0-0" \
   -i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
   -o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt”

这给出了有关下载缓存的错误消息：

IMPORTANT INFORMATION:
The VEP can read gene data from either a local cache or local/remote databases.

或者这个：

vep --cache \
   -i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
   -o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt”

这给出了错误：

MSG: ERROR: Cache directory /mnt/gpfs/home/skgtmdf/.vep/homo_sapiens not found

我想没有人能给我指出正确的方向吗？

Answer 1

我找到了答案。您需要同时添加 --cache 和 --dir_cache 参数：

vep --cache --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105.0-0" \
   -i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
   -o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt"

如何在 conda 中运行 ensembl-vep

How to run ensembl-vep in conda

variant

vcftools

vcf-variant-call-format

gatk

如何在 conda 中 运行 ensembl-vep

How to run ensembl-vep in conda

variant

vcftools

vcf-variant-call-format

gatk

如何在 conda 中运行 ensembl-vep