--acmg not working

[SouzaBB]

I'm trying to use the --acmg flag but having the following issue

command is: python3 tapes.py sort -i ./VCFs_teste/Sample.vep.vcf -o VCFs_teste/out_files/ --tab --acmg --by_gene -a hg19

No acmg_db path given and no db_config.json found
Default is: /path/to/tapes/acmg_db

        ***TAPES: SORT***

2020-11-09 11:58:58.....Output type: FOLDER
2020-11-09 11:58:58.....VEP vcf processing 2020-11-09 11:58:58.....Only one sample found in vcf
Done
2020-11-09 11:58:58.....vep annotated file
2020-11-09 11:58:58.....Gene annotation : refGene
|| No sample data found
2020-11-09 11:58:58.....All required annotations not found. Try to remove the --acmg tag
2020-11-09 11:58:58.....EXITING

I'm using all annotations required in my vep output but this error always shows up when using --acmg flag.

I'm also using dbnsfp plugins as follows:

--plugin dbNSFP,/path/to/dbNSFPv3.5a_hg19.gz,gnomAD_genomes_AF,gnomAD_exomes_AF,CADD_phred,FATHMM_converted_rankscore,clinvar_clnsig,clinvar_golden_stars,Interpro_domain,SIFT_score,LRT_pred,MutationTaster_pred,MutationAssessor_pred,FATHMM_pred,PROVEAN_score,MetaSVM_pred,MetaLR_pred,M-CAP_pred,fathmm-MKL_coding_pred,GenoCanyon_score,GERP++_RS

And dbscSNV:

--plugin dbscSNV,/path/to/dbscSNV1.1_GRCh37.txt.gz

Does anyone know how to solve this?

Thanks.

[KeyTals]

I am getting the same error with hg38. Any update regarding this issue yet?

Keyur

[SouzaBB]

Hi @KeyTals, not yet.. Still trying to figure out what is happening!

[KeyTals]

Its not working with VEP but working fine with Annovar. I think issue is the annotations required (cloumn names ) are hard coded as per Annovar.

[lmanchon]

Many of us are experiencing problems with Tapes and poor annotation by VEP. It would be helpful if the author would decide to give us a concrete example of a command line that works for VEP!

[SouzaBB]

It seems that the author is not maintaining this tool anymore. Years without a single update. It's sad because it's actually a great tool!