Persistent Warning Regarding INFO/IMPORT_FAIL in VCF Header

[Iredcg]

Hello,

I’ve been using hap.py to benchmark two VCF files, but I keep encountering the following warning:
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Number=0

I’ve tried modifying the VCF header to ensure the IMPORT_FAIL field is defined correctly as Number=0 and Type=Flag. Despite this, the warning persists. I’ve also attempted to compare two VCF files, ensuring their headers are consistent, but I’m still seeing this issue.

Could you please provide guidance on how hap.py handles the IMPORT_FAIL flag, or any further suggestions to resolve this issue?

Thank you for your assistance.

Best regards,
Irene

[rodrigodealexandre]

I am having the same issue.
A samples processed with Dragen 4.3.6 running with simple arguments such as:

hap.py "$GOLD_STANDARD_VCF" "$INPUT_VCF" \
  -f "$GOLD_STANDARD_BED" \
  -o "$OUTPUT_PREFIX" \
  -r "$REFERENCE_FASTA" \
  -V

this command is been run on a conda environment after hap.py installation with:

conda create -n bioinfo_happy python=2.7
conda install -c bioconda hap.py
conda install -c conda-forge bcftools=1.10

there had been no modification in the VCF file after Dragen output.
the docker installation does not shows this warning for the same file.

Thanks,
Rodrigo

[gianfilippo]

same here