VEP run statistics
| VEP version (API) | 104 (104) |
| Annotation sources | Cache: /scg/apps/data/refgenomes/CanFam3.1/release-104/index/ensembl-vep/104.3/cache/canis_lupus_familiaris/104_CanFam3.1; canis_lupus_familiaris_core_104_31 on ensembldb.ensembl.org |
| Species | canis_lupus_familiaris |
| Command line options | --assembly CanFam3.1 --cache --compress_output bgzip --dir_cache /scg/apps/data/refgenomes/CanFam3.1/release-104/index/ensembl-vep/104.3/cache --dir_plugins /scg/apps/data/refgenomes/CanFam3.1/release-104/index/ensembl-vep/104.3/cache/plugins --everything --fasta /scg/apps/data/refgenomes/CanFam3.1/release-104/Canis_lupus_familiaris.CanFam3.1.dna_sm.toplevel.fa --format vcf --input_file /oak/stanford/scg/lab_sherril/BaaS/kllucot/wgs/pacbio/Analyses/VariantCalling/Sentieon/B49/B49_all_variants.vcf.gz --output_file /labs/sherril/BaaS/kllucot/wgs/pacbio/Analyses/Annotation/VEP/B49_VEP_annotated_with_phenotypes.vcf.gz --plugin Phenotypes,dir=/scg/apps/data/refgenomes/CanFam3.1/release-104/index/ensembl-vep/104.3/cache/plugins,include_types=Gene --species canis_lupus_familiaris |
| Start time | 2021-12-15 13:15:09 |
| End time | 2021-12-15 16:21:09 |
| Run time | 11160 seconds |
| Input file | /oak/stanford/scg/lab_sherril/BaaS/kllucot/wgs/pacbio/Analyses/VariantCalling/Sentieon/B49/B49_all_variants.vcf.gz |
| Output file | /labs/sherril/BaaS/kllucot/wgs/pacbio/Analyses/Annotation/VEP/B49_VEP_annotated_with_phenotypes.vcf.gz |
General statistics
| Lines of input read | 6460969 |
| Variants processed | 6460969 |
| Variants filtered out | 0 |
| Novel / existing variants | 3957690 (61.3) / 2503279 (38.7) |
| Overlapped genes | 30385 |
| Overlapped transcripts | 60220 |
| Overlapped regulatory features | 0 |
