Running vcf2maf WARNING: No genotype column for NORMAL in VCF! WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!

[tanayb001]

Hi,
I am running vcf2maf to annotate my VCF file and convert it into MAF file. However I am getting these warnings and my VCF file doesn't have any genotype column. The vcf files are generated using Mutect2 using matched normal samples.
Here is the full run:

perl vcf2maf.pl --input-vcf PH01.PON.somatic.filtered.PASS.vcf --output-maf PH01.PON.somatic.filtered.PASS.maf --tumor-id PH01-TD normal-id PH01-BD --ncbi-build GRCh38 --ref-fasta hg38.fa --vep-path /Toolkit/ensembl-vep-build

STATUS: Running VEP and writing to: /media/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e2/passed/PH01.PON.somatic.filtered.PASS.vep.vcf
WARNING: No genotype column for NORMAL in VCF!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized effect "splice_polypyrimidine_tract_variant". Assigning lowest priority!
WARNING: Unrecognized effect "splice_polypyrimidine_tract_variant". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized effect "splice_donor_5th_base_variant". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!
WARNING: Unrecognized biotype "protein_coding_CDS_not_defined". Assigning lowest priority!

Please let me know what should I do and how do I get the genotype information.

Thanks,

Regards,
Tanay

[maciejmotyka]

For the explanation of what the "Unrecognized biotype" warnings mean and where do they come from see issue #349