Warnings appear when running with a VEP-annotated input file

[paulhtyang]

Hello,

We got the warnings when running with a VEP-annotated VCF or MAF files. Here are the details:

charger -f ../../software/vcf2maf-1.6.16/gnomAD_APC_maf.vep.vcf -o APC_charger.tsv --PP2GeneList PP2.genes.hg19 --BP1GeneList BP1.genes.hg19 -H APC_inp.maf.3D_Proximity.pairwise.site.l0.ad10.r20.clusters -D --inheritanceGeneList inheritanceGeneList.txt --exac-vcf ~pyang/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz --mac-clinvar-tsv ./clinvar_alleles.single.b37.tsv.gz
Using default module scores and category thresholds:
   BA1 = -8
   BMC1 = -2
   BP1 = -1
   BP2 = -1
   BP3 = -1
   BP4 = -1
   BP5 = -1
   BP6 = -1
   BP7 = -1
   BS1 = -4
   BS2 = -4
   BS3 = -4
   BS4 = -4
   BSC1 = -6
   PM1 = 2
   PM2 = 2
   PM3 = 2
   PM4 = 2
   PM5 = 2
   PM6 = 2
   PMC1 = 2
   PP1 = 1
   PP2 = 1
   PP3 = 1
   PP4 = 1
   PP5 = 1
   PPC1 = 1
   PPC2 = 1
   PS1 = 7
   PS2 = 4
   PS3 = 4
   PS4 = 4
   PSC1 = 4
   PVS1 = 8
   maxBenignScore = -8
   maxLikelyBenignScore = -4
   minLikelyPathogenicScore = 5
   minPathogenicScore = 9
Will capture vcf details for output: False
This .vcf has VEP annotations!
biomine::variant::mafvariant Warning: could not find amino acid change or intronic change
  Hint: Is the input amino acid change column correct?
    Problem variant:  :None:None-None->-:::c.:::p.  --  p.Pro9=
biomine::variant::mafvariant Warning: could not find amino acid change or intronic change
  Hint: Is the input amino acid change column correct?
    Problem variant:  :None:None-None->-:::c.:::p.  --  p.Val10=
biomine::variant::mafvariant Warning: could not find amino acid change or intronic change
  Hint: Is the input amino acid change column correct?
    Problem variant:  :None:None-None->-:::c.:::p.  --  p.Pro14=
biomine::variant::mafvariant Warning: could not find amino acid change or intronic change
  Hint: Is the input amino acid change column correct?
    Problem variant:  :None:None-None->-:::c.:::p.  --  p.Pro14=

Why "charger" is trying to access "biomine" because the input file already has VEP annotations? Moreover, our input file is limited to a gene, i.e. APC, but the standard outputs (see the enclosed file test.log) with warning appear to have many genes included.

Thanks for your helps.

[nroak]

I'm experiencing the same issue. What modifications to the input are needed to ensure this is read correctly? Does running a b38 based variant list lead to this issue? Is there a way to provide a reference assembly version?

[fernanda-rodrigues]

@paulhtyang and @nroak I apologize for the delay on getting to this issue. As of right now, you can ignore these warnings; after testing, they do not seem to affect the results. However, I am working on the issue and will post an update here as soon as possible.

Thanks! Fernanda

[nroak]

Thank you, Fernanda, for the response. good to know that these can be ignored.

[fernanda-rodrigues]

Issue has been solved in ding-lab/BioMine. Please refer to ding-lab/BioMine commit c33c77c for changes. https://github.com/ding-lab/BioMine/commit/c33c77c6f965075e4c16866ad0d832c047aeddb3

Please reinstall CharGer for changes to take place.