Description
Dear Developer Team,
I am using VEP to annotate mouse structural variant calls from delly. The annotation seems unclear. For example, I get a deletion call from delly which looks like this in the VCF file:
GRanges object with 1 range and 5 metadata columns:
seqnames ranges strand | paramRangeID REF ALT QUAL FILTER
|
DEL00062627 chr7 60036293 * | NA A 3364 PASS
seqinfo: 61 sequences from an unspecified genome
info(vcf_list[[11]][names(rowRanges(vcf_list[[11]])) == 'DEL00062627',])
DataFrame with 1 row and 21 columns
CIEND CIPOS CHR2 POS2 END PE MAPQ SRMAPQ SR SRQ CONSENSUS CONSBP CE CT SVLEN IMPRECISE
DEL00062627 -50,50 -50,50 NA NA 60137265 65 54 NA NA NA NA NA NA 3to5 NA TRUE
PRECISE SVTYPE SVMETHOD INSLEN HOMLEN
DEL00062627 FALSE DEL EMBL.DELLYv1.3.3 NA NA
The annotation for this call from VEP looks like this:
X.Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position
16171250 DEL00062627 chr7:60036294-60137265 deletion ENSMUSG00000000538 ENSMUST00000133420 Transcript transcript_ablation - -
16171264 DEL00062627 chr7:60036294-60137265 deletion ENSMUSG00000000538 ENSMUST00000143124 Transcript transcript_ablation - -
16171274 DEL00062627 chr7:60036294-60137265 deletion ENSMUSG00000000538 ENSMUST00000151284 Transcript transcript_ablation - -
16171276 DEL00062627 chr7:60036294-60137265 deletion ENSMUSG00000000538 ENSMUST00000153920 Transcript transcript_ablation - -
Protein_position Amino_acids Codons Existing_variation Extra
16171250 - - - - IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;OverlapBP=15256;OverlapPC=100.00
16171264 - - - - IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;OverlapBP=15768;OverlapPC=100.00
16171274 - - - - IMPACT=HIGH;STRAND=-1;OverlapBP=1745;OverlapPC=100.00
16171276 - - - - IMPACT=HIGH;STRAND=-1;OverlapBP=12462;OverlapPC=100.00
Then when I convert the ENSEMBL gene ID ENSMUSG00000000538 to gene symbol I get this gene TOM1L2 located in chr11 in mice. Could the deletion in chr7 affect this gene?
System
- VEP version: v113.0
- VEP Cache version: vep_data/mus_musculus/113_GRCm39
- OS: Ubuntu
Full VEP command line
module load singularityce
for vcffile in $HOME/vep_data/vep_hspc/input_hspc/Etoposide_Transform*.vcf; do
vcfname=$(basename $vcffile .vcf)
singularity exec vep.sif
vep --dir $HOME/vep_data
--cache --offline --force_overwrite --species mus_musculus
--input_file vep_data/vep_hspc/input_hspc/$vcfname.vcf
--output_file vep_data/vep_hspc/output_hspc/$vcfname.vep.txt
--plugin NMD
wait -n
done
Thanks in advance,
Karolina