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VEP run statistics

VEP version (API) 106 (106)
Annotation sourcesCache: /.vep/homo_sapiens/106_GRCh38
Specieshomo_sapiens
Command line options
--assembly GRCh38 --cache --cache_version 106 --dir_cache /.vep --everything --filter_common --fork 6 --format vcf --input_file HG00138N.haplotypecaller.filtered.vcf.gz --offline --output_file HG00138N.haplotypecaller.filtered_VEP.ann.vcf --per_gene --plugin dbNSFP,consequence=ALL,dbNSFP4.2a_grch38.gz,rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF --plugin LoF --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz --plugin SpliceRegion --species homo_sapiens --stats_file HG00138N.haplotypecaller.filtered_VEP.summary.html --total_length --vcf
Start time2022-07-25 12:51:16
End time2022-07-25 12:53:16
Run time120 seconds
Input fileHG00138N.haplotypecaller.filtered.vcf.gz
Output fileHG00138N.haplotypecaller.filtered_VEP.ann.vcf

General statistics

Lines of input read51557
Variants processed25102
Variants filtered out26455
Novel / existing variants0 (0.0) / 25102 (100.0)
Overlapped genes1288
Overlapped transcripts1444
Overlapped regulatory features3090

Variant classes

 
 

Consequences (most severe)

 
 

Consequences (all)

 
 

Coding consequences

 
 

SIFT summary

 
 

PolyPhen summary

 
 

Variants by chromosome

 
 

Position in protein