I have 24 LoF suspected variants which I'm trying to annotate using LOFTEE. For 14 out of 24 variants, there is LoF annotation for at least one transcript in the "Extra" column like follows.
[In the case of NM_013266.4:c.1219delC]
Feature "ENST00000494580" is annotated as "IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;LoF=LC;LoF_filter=END_TRUNC;LoF_info=GERP_DIST:0--" in the Column "Extra".
However, for the rest of the variants (10 variants marked with stars* below), there is no LoF annotation for any of the transcripts, although the consequence is indeed LoF suspected (eg. frameshift).
Does anyone have an explanation for this?
the input command is "./vep --species homo_sapiens --assembly GRCh38 --database --plugin LoF,loftee_path:$HOME/ensembl-vep/loftee,human_ancestor_fa:$HOME/ensembl-vep/human_ancestor.fa -i $HOME/ensembl-vep/LoF_hgvs_c_info.txt -o $HOME/ensembl-vep/LoF_hgvs_c_LOFTEE_result".
I have 24 LoF suspected variants which I'm trying to annotate using LOFTEE. For 14 out of 24 variants, there is LoF annotation for at least one transcript in the "Extra" column like follows.
[In the case of NM_013266.4:c.1219delC] Feature "ENST00000494580" is annotated as "IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;LoF=LC;LoF_filter=END_TRUNC;LoF_info=GERP_DIST:0--" in the Column "Extra".
However, for the rest of the variants (10 variants marked with stars* below), there is no LoF annotation for any of the transcripts, although the consequence is indeed LoF suspected (eg. frameshift).
Does anyone have an explanation for this?
the input command is "./vep --species homo_sapiens --assembly GRCh38 --database --plugin LoF,loftee_path:$HOME/ensembl-vep/loftee,human_ancestor_fa:$HOME/ensembl-vep/human_ancestor.fa -i $HOME/ensembl-vep/LoF_hgvs_c_info.txt -o $HOME/ensembl-vep/LoF_hgvs_c_LOFTEE_result".
Thanks.
NM_001035.3:c.14217delT NM_013266.4:c.1219delC NM_004387.4:c.335-204delT NM_053025.4:c.1654C>T NM_004572.4:c.148_151delACAG NM_001267550.2:c.36364+1G>C NM_020778.5:c.2304delA NM_000527.5:c.2431A>T NM_001267550.2:c.44281+1G>C NM_001267550.2:c.4764_4765dupAT NM_000488.4:c.762+69dupT NM_020778.5:c.2304delA NM_012186.3:c.432C>G NM_013266.4:c.560dupT NM_001267550.2:c.36364+1G>C NM_003476.5:c.583T>A NM_001267550.2:c.47208_47209delCA NM_001267550.2:c.36364+1G>C NM_032578.4:c.3796C>T NM_000256.3:c.890C>G NM_004387.4:c.335-163_335-157dupCGGTGGC NM_174936.4:c.1284G>A NM_020297.4:c.1659+1delG NM_013266.4:c.560dupT LoF_hgvs_c_info.txt LoF_hgvs_c_LOFTEE_result.xlsx