How can I get other parameters from Ensembl VEP for vcf annotation
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4.1 years ago
mittu1602 ▴ 180

Hello all, I am using Ensembl VEP for annotating my vcf file with the following commands:

> perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh37 --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --input_file sample.vcf  --output_file sample.vep.vcf --polyphen b --gmaf --maf_1kg --maf_esp --regulatory --custom ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz,ExAC,vcf,exact,1,AC,AN

and then converting it to maf file by:

> perl vcf2maf.pl --vep-path /home/explore/vep/ --vep-data /home/explore/.vep/  --ref-fasta /home/explore/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz  --input-vcf sample.vcf  --tumor-id Human --output-maf /sample.vep.maf

I specifically get these 3 columns blank:

t_depth t_ref_count t_alt_count

If anyone can tell what am I missing?? Thank you!

EDIT: It is solved, by changing the file type.

variant type snps • 1.7k views
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Entering edit mode

@Emily_Ensembl can you please have a look

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