A "extra_vep_options" specifically for SV?

[A97paupic]

Description of feature

Hi, would it be possible to add an "extra_vep_options" specifically for SV so that one can separate between SNV and SV specific arguments? At the moment the ANNOTATE_SVS:ENSEMBLVEP_SV process will fail whenever I add arguments specific to SNV annotation. Thanks in advance!

Kind Regards,
Paul

[fellen31]

Hi Paul, I agree there should be an easier way to add arguments to VEP. extra_vep_options was mainly added for the test profile, but it could be changed into adding extra arguments for SNVs and SVs separately as you suggest. A problem with using params might be if you need to remove or change something that is in nallo by default.

In the meantime, you can achieve similar results by supplying a config file that overrides the default settings, copying the default arguments from nallo and then modifying them to fit your needs, e.g.:

process {
    withName: '.*:ANNOTATE_SVS:ENSEMBLVEP_SV' {
        ext.args = [
          '--dir_plugins .',
          '--plugin pLI,grch38_vep_112_pli_values_-v1.0-.txt',
          '--distance 5000',
          '--buffer_size 5000',
          '--format vcf --max_sv_size 248387328',
          '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
          '--domains --exclude_predicted --force_overwrite',
          '--hgvs --humdiv --no_progress --numbers',
          '--per_gene',
          '--polyphen p --protein --offline --sift p --regulatory --symbol --tsl',
          '--uniprot --vcf',
          '--no_stats',
          '--merged'
        ].join(' ')
    }
    withName: '.*:SNV_ANNOTATION:ENSEMBLVEP_SNV' {
        ext.args = [
            '--dir_plugins .',
            '--plugin LoFtool,grch38_vep_112_loftool_scores_-v1.0-.txt',
            '--plugin pLI,grch38_vep_112_pli_values_-v1.0-.txt',
            '--plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz',
            '--distance 5000',
            '--buffer_size 20000',
            '--format vcf --max_sv_size 248387328',
            '--appris --biotype --cache --canonical --ccds --compress_output bgzip',
            '--domains --exclude_predicted --force_overwrite',
            '--hgvs --humdiv --no_progress --numbers',
            '--polyphen p --protein --offline --regulatory --sift p --symbol --tsl',
            '--uniprot --vcf',
            '--no_stats',
            '--merged',
            '--custom grch38_clinvar_20250217_renamed_reformatted.vcf.gz,CLINVAR,vcf,exact,0,CLNSIG,CLNVID,CLNREVSTAT'
        ].join(' ')
    }
}

[A97paupic]

Thanks, I will try supplying it to a config file!

Kind Regards,
Paul

[fellen31]

You might be interested in checking out genomic-medicine-sweden/nallorefs#1 as well, trying to explain more or less exactly how Nallo is run in Uppsala/Stockholm at the moment.