bcftools - issue when trying to merge two VCFs

[AshleyShi2000]

I'm getting this error when trying to merge my two VCF files. I first used bgzip to compress my files and then indexed them before merging.
Not ready for type [0]: SNP at 82113

Thanks for helping!

[pd3]

That's indeed a very cryptic message, did not expect to ever encounter such case. Could you please check the headers and show which the tags are defined as Number=G/A/R? A small test case to reproduce the problem would be really helpful here.

[AshleyShi2000]

I've uploaded the original files to OneDrive!
https://1drv.ms/u/s!AuZRdpWMK4MxgUVCAKTE_X6r9Y5a?e=JJ3vfe

These are the commands that I used:
bgzip -c DTB-003.vcf > DTB003.vcf.gz
bcftools index DTB003.vcf.gz
bgzip -c DTB-005.vcf > DTB005.vcf.gz
bcftools index DTB005.vcf.gz
bcftools merge DTB003.vcf.gz DTB005.vcf.gz > merged.vcf
Not ready for type [0]: SNP at 82113

The tags that are defined as Number=A are:
##INFO=<ID=VARTYPE,Number=A,Type=String,Description="Comma separated list of variant types. One per allele">
##INFO=<ID=SNP,Number=A,Type=Flag,Description="Variant is a SNP">
##INFO=<ID=MNP,Number=A,Type=Flag,Description="Variant is a MNP">
##INFO=<ID=INS,Number=A,Type=Flag,Description="Variant is a INS">
##INFO=<ID=DEL,Number=A,Type=Flag,Description="Variant is a DEL">
##INFO=<ID=MIXED,Number=A,Type=Flag,Description="Variant is a MIXED">
##INFO=<ID=HOM,Number=A,Type=Flag,Description="Variant is homozygous">
##INFO=<ID=HET,Number=A,Type=Flag,Description="Variant is heterozygous">

I hope these are what you're looking for. Thanks again for your kind help!

[pd3]

Thank you for the test files. The problem is caused by flag types being defined as Number=A. This violates the VCF specification which explicitly states that

The ‘Flag’ type indicates that the INFO field does not contain a Value entry, and hence the Number must be 0
in this case.

An easy workaround should be to fix the header

bcftools view -h file.bcf > hdr.txt
# edit the header and change all Type=Flag tags to Number=0
bcftools reheader -h hdr.txt file.bcf -o fixed.bcf

Ideally the program that produced the VCFs should be fixed.

[pd3]

After this pull request is fixed samtools/htslib#1415, bcftools will be able to work with such files.

Note that it is only a workaround, this should really be addressed at the VCF producer side.

[pd3]

This is now merged via samtools/htslib#1415