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VEP run statistics

VEP version (API) 103 (103)
Annotation sourcesCache: /tmp/vep-ensembl-103.1/.vep/homo_sapiens/103_GRCh38; homo_sapiens_core_103_38 on ensembldb.ensembl.org; Custom: /tmp/dm1/annotationData/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz (exact); Custom: /tmp/dm1/annotationData/clinvar.hg38.vcf.gz (exact)
Specieshomo_sapiens
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/M0239-case-Joubert-8155-3/M0239-case-Joubert-8155-3.guppy5012.minimap2.clair3.targetsOnly.vcf --max_af --numbers --output_file /net/eichler/vol27/projects/clinicalLongReadSeq/nobackups/alignments/M0239-case-Joubert-8155-3/M0239-case-Joubert-8155-3.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
Start time2021-10-11 06:37:55
End time2021-10-11 07:47:59
Run time4204 seconds
Input file/net/eichler/vol27/projects/clinicalLongReadSeq/nobackups/alignments/M0239-case-Joubert-8155-3/M0239-case-Joubert-8155-3.guppy5012.minimap2.clair3.targetsOnly.vcf
Output file/net/eichler/vol27/projects/clinicalLongReadSeq/nobackups/alignments/M0239-case-Joubert-8155-3/M0239-case-Joubert-8155-3.guppy5012.minimap2.clair3.targetsOnly.VEP.vcf

General statistics

Lines of input read31581
Variants processed31581
Variants filtered out0
Novel / existing variants3335 (10.6) / 28246 (89.4)
Overlapped genes412
Overlapped transcripts461
Overlapped regulatory features280

Variant classes

 
 

Consequences (most severe)

 
 

Consequences (all)

 
 

Coding consequences

 
 

SIFT summary

 
 

PolyPhen summary

 
 

Variants by chromosome

 
 

Position in protein