Conserv CSQ and output plugin

Question

[robertclerc]

Hello,

I am trying to use the CSQ annotation produced by VEP with that of the biomart plugin. However, the CSQ annotation overwrites that of MaxEntScan.

A Example of a variant with MaxEntScan only :

Commande line

/vep -i file_in.vcf -o out_annoted_MES_only.vcf.gz --keep_csq --fasta /data2/Homo_sapiens.GRCh37.74.dna.primary_assembly.fa.gz --offline --force_overwrite --compress_output bgzip --assembly GRCh37 --plugin MaxEntScan,/data2/MaxEntScan/fordownload`

Output

rs132876 chr22:45567035 T ENSG00000093000 ENST00000417702 Transcript splice_donor_variant - - - - -- IMPACT=HIGH;STRAND=1;FLAGS=cds_end_NF;MaxEntScan_alt=5.122;MaxEntScan_diff=-7.754;MaxEntScan_ref=-2.632

It's possible to see the MaxEntScan scoring.

And a example with MaxEntScan and VEP

Commande line

./vep -i file_in.vcf -o out_annoted_MES.vcf.gz --keep_csq --fasta /data2/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --offline --force_overwrite --compress_output bgzip --assembly GRCh37 --vcf CSQ --fields Uploaded_variation,Gene,Feature,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,STRAND --plugin MaxEntScan,/data2/MaxEntScan/fordownload

Output

rs132876 C T 124.77 . AC=1;AF=0.5;AN=2;ANN=T|splice_donor_variant& ... 32876|ENSG00000093000|ENST00000491860|upstream_transcript_variant||||||1,rs132876|ENSG00000093000|ENST00000497960|intron_variant&non_coding_transcript_variant||||||1 GT:PL:PGT:GQ:DP:AD:PID 0/1:153,0,352:0|1:99:9:5,4:45567035_C_T .

The CSQ annotation overwrite the MaxEntScan scoring. How it's possible to have the scoring of MaxEntScan and the CSQ annotation ?

[GenoMax]

Tagging: Emily_Ensembl
Ben_Ensembl

[Emily]

Tagging me doesn't do anything.

Answer 1

[Emily]

The reason you're losing the MaxEntScan fields is that you didn't specify them with --fields. You can run without --fields and you'll get the data, or you can run with it and specify the MaxEntScan fields too.

./vep -i input.vcf -o output.vcf --plugin MaxEntScan,/data2/MaxEntScan/fordownload -vcf

or

./vep -i input.vcf -o output.vcf --plugin MaxEntScan,/data2/MaxEntScan/fordownload -vcf -fields Uploaded_variation,Gene,Feature,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,STRAND,MaxEntScan_diff