#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS SYMBOL SYMBOL_SOURCE HGNC_ID LoF LoF_filter LoF_flags LoF_info
7_117642566_G/A 7:117642566 A ENSG00000001626 ENST00000003084 Transcript stop_gained 3916 3846 1282 W/* tgG/tgA - HIGH - 1 - CFTR HGNC HGNC:1884 - - - -
I did not find phylocsf_gerp.sql.gz for GRCh38.
command used-
VEP command-line:
vep --assembly GRCh38 --cache --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/Plugins/ --fasta [PATH]/Homo_sapiens_assembly38cleaned.fasta --force_overwrite --input_file test_lof_grch38.vcf --offline --output_file test_lof_annot.txt --pick --plugin LoF,[PATH]/loftee,[PATH]/human_ancestor_hg38.fa.gz,[PATH]/loftee.sql,[PATH]/gerp_conservation_scores.bw --symbol --tab --verbose
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS SYMBOL SYMBOL_SOURCE HGNC_ID LoF LoF_filter LoF_flags LoF_info
7_117642566_G/A 7:117642566 A ENSG00000001626 ENST00000003084 Transcript stop_gained 3916 3846 1282 W/* tgG/tgA - HIGH - 1 - CFTR HGNC HGNC:1884 - - - -
I did not find phylocsf_gerp.sql.gz for GRCh38.
command used-
VEP command-line:
vep --assembly GRCh38 --cache --database 0 --dir_cache [PATH]/cache --dir_plugins [PATH]/Plugins/ --fasta [PATH]/Homo_sapiens_assembly38cleaned.fasta --force_overwrite --input_file test_lof_grch38.vcf --offline --output_file test_lof_annot.txt --pick --plugin LoF,[PATH]/loftee,[PATH]/human_ancestor_hg38.fa.gz,[PATH]/loftee.sql,[PATH]/gerp_conservation_scores.bw --symbol --tab --verbose