Failed to run vcf2maf for a vcf file cleaned with vcf2vcf

[wisekh6]

Hello,

I applied vcf2maf to a vcf file cleaned with vcf2vcf. The original vcf was an output from pindel. I have the following error from running vcf2maf. Would you please help me to successfully run vcf2maf?

Thank you in advance,

STATUS: Running VEP and writing to: /home/test/clean_pindel_vcf/12A_CTTGTA_na__12C_CTTGTA_na.cleaned.vep.vcf

Running following vep command
perl /home/vep/ensembl-vep/vep --species homo_sapiens --assembly GRCh37 --offline --no
_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --var
iant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,
length --dir /home/vep/v91 --fasta /home/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta --format vcf --input_file /project
s/kimh/GLASS/pipeline/flowr/pindel/v1.0/test/clean_pindel_vcf/12A_CTTGTA_na__12C_CTTGTA_na.cleaned.vcf --output_file /home/test
/clean_pindel_vcf/12A_CTTGTA_na__12C_CTTGTA_na.cleaned.vep.vcf --fork 5 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory
------------
    WARNING: VCF line on line 26672 looks incomplete, skipping:
    1       121116646       .       T       <DEL>   .       .               GT:AD:DP        0/0:153,6:159   0/0:60,1:61
Can't locate object method "variation_feature_seq" via package "Bio::EnsEMBL::Variation::TranscriptStructuralVariationAllele" at /home/vep/e
nsembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 568.
Died in forked process 5971

ERROR: Failed to run the VEP annotator! Command: perl /home/vep/ensembl-vep/vep --spec
ies homo_sapiens --assembly GRCh37 --offline --no_progress --no_stats --buffer_size 5000 --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 --flag_pick_all
ele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /home/vep/v91 --fasta /home/gatk-legacy-bundles/b37/human_g1k_v
37_decoy.fasta --format vcf --input_file /home/test/clean_pindel_vcf/12A_CTTGTA_na__12C_CTTGTA_na.cleaned.vcf --output_file /home/test/clean_pindel_vcf/12A_CTTGTA_na__12C_CTTGTA_na.cleaned.vep.vcf --fork 5 --polyphen b --af --af_1kg --af_esp --af_gnomad
--regulatory

[fpbarthel]

@wisekh6 it looks like this is related --flag_pick_allele parameter and was fixed in VEP 92.5, see: https://github.com/Ensembl/ensembl-vep/issues/227