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Description Hi,
docker run -v /home/dnanexus:/opt/data matmu/vep:105-GRCh37 vep --dir /opt/vep/.vep --offline --cache --input_file /opt/data/NGC00142_01.vcf.gz --vcf -o STDOUT --format vcf --offline --cache --dir_cache /opt/data/snv-master/demo/softwares/vep/grch37 --force_overwrite --species homo_sapiens --assembly GRCh37 --port 3337 --vcf_info_field ANN --sift b --polyphen b --humdiv --regulatory --allele_number --total_length --numbers --domains --hgvs --protein --symbol --ccds --uniprot --canonical --biotype --check_existing --af --af_1kg --pubmed --gene_phenotype --variant_class --plugin CADD,/opt/data/snv-master/demo/resources/cadd/grch37/whole_genome_SNVs.tsv.gz,/opt/data/snv-master/demo/resources/cadd/grch37/InDels.tsv.gz --plugin ExACpLI,/opt/data/snv-master/demo/resources/gnomad/grch37/gnomad.v2.1.1.lof_metrics.by_transcript_forVEP.txt --plugin REVEL,/opt/data/snv-master/demo/resources/revel/grch37/new_tabbed_revel.tsv.gz --plugin SpliceRegion --stats_text --stats_file /opt/data/tmpFile_1_AC0.exon.noGT.vep_stats.txt --output_file /opt/data/tmpFile_1_AC0.exon.noGT.new.vep.vcf
But, getting the following error:
Please let me know how to fix it.
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Hi,
I am trying to run VEP using this docker command:
docker run -v /home/dnanexus:/opt/data matmu/vep:105-GRCh37 vep --dir /opt/vep/.vep --offline --cache --input_file /opt/data/NGC00142_01.vcf.gz --vcf -o STDOUT --format vcf --offline --cache --dir_cache /opt/data/snv-master/demo/softwares/vep/grch37 --force_overwrite --species homo_sapiens --assembly GRCh37 --port 3337 --vcf_info_field ANN --sift b --polyphen b --humdiv --regulatory --allele_number --total_length --numbers --domains --hgvs --protein --symbol --ccds --uniprot --canonical --biotype --check_existing --af --af_1kg --pubmed --gene_phenotype --variant_class --plugin CADD,/opt/data/snv-master/demo/resources/cadd/grch37/whole_genome_SNVs.tsv.gz,/opt/data/snv-master/demo/resources/cadd/grch37/InDels.tsv.gz --plugin ExACpLI,/opt/data/snv-master/demo/resources/gnomad/grch37/gnomad.v2.1.1.lof_metrics.by_transcript_forVEP.txt --plugin REVEL,/opt/data/snv-master/demo/resources/revel/grch37/new_tabbed_revel.tsv.gz --plugin SpliceRegion --stats_text --stats_file /opt/data/tmpFile_1_AC0.exon.noGT.vep_stats.txt --output_file /opt/data/tmpFile_1_AC0.exon.noGT.new.vep.vcfBut, getting the following error:
Please let me know how to fix it.
Thanks with regards,
Ravi