I encountered an error running VEP (v81) which I have not encountered before. Error states:
E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "#chr pos(1-based) ref alt ...
This is 0% into a 'calculating consequences' step. I am unsure if VEP has not annotated anything for chromosome it was operating on (although below the error is a 100% progress bar and time has been taken after this error). Also not sure what the -p [type] refers to(?)
My command is:
perl variant_effect_predictor.pl --force_overwrite --offline --cache \ --no_stats --everything --check_existing --total_length --allele_number \ --no_escape --gencode_basic --vcf --merged -custom /bin/GERP/All_hg19_RS.bw,GERP,bigwig \ --plugin dbNSFP,/bin/dbNSFP/dbNSFP.gz,1000Gp3_EUR_AF,ESP6500_EA_AF,SIFT_score,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_pred,LRT_score,LRT_pred,MutationTaster_score,MutationTaster_pred \ --pick_order biotype,tsl,canonical,length,ccds,rank \ --input_file $inp --output_file $out
which has worked for other VCF before.
Any thoughts are greatly appreciated, mainly I want to know if this is a tolerable error for single position, or more likely to be something requiring a fix and rerun.