| Command line options | --af --af_1kg --cache --canonical --custom /tmp/dm1/annotationData/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz,gnomADg,vcf,exact,0,AF --custom /tmp/dm1/annotationData/clinvar.hg38.vcf.gz,ClinVar,vcf,exact,0,CLINSIG,CLNREVSTAT,CLNDN --dir_cache /tmp/vep-ensembl-103.1/.vep --dir_plugins /tmp/vep-ensembl-103.1/.vep/Plugins --domains --force_overwrite --input_file /net/eichler/vol27/projects/clinicalLongReadSeq/nobackups/alignments/M0232-case-9367-3-CNV/M0232-case-9367-3-CNV.guppy5012.minimap2.clair3.targetsOnly.vcf --max_af --numbers --output_file /net/eichler/vol27/projects/clinicalLongReadSeq/nobackups/alignments/M0232-case-9367-3-CNV/M0232-case-9367-3-CNV.guppy5012.minimap2.clair3.targetsOnly.VEP.vcf --pick --plugin CADD,/tmp/dm1/annotationData/CADDv1.6_hg38_whole_genome_SNVs.tsv.gz --plugin SpliceAI,snv=/tmp/dm1/annotationData/spliceai_scores.raw.snv.hg38.vcf.gz,indel=/tmp/dm1/annotationData/spliceai_scores.raw.indel.hg38.vcf.gz --polyphen b --pubmed --regulatory --sift b --symbol --total_length --vcf |
