Merge VCF files using bcftools merge

Question

[lisadavic66]

Dear All,

I am using bcftools to combine 3 VCF files with following command:

bcftools merge -m snps -O v -o merged.vcf a.vcf.gz b.vcf.gz c.vcf.gz

but got these kind of error information:

[E::get_intv] failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: "##fileformat=VCFv4.2"
[E::get_intv] failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: "##fileformat=VCFv4.2"
[E::get_intv] failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: "##fileformat=VCFv4.2"

I don't know what does this mean and how to solve the problem. Can anybody help me out? Thank you in advance.

[Danielk]

Are the index file .tbi present?

Answer 1

[ebrown1955]

Check your version of bcftools. It may be outdated, as VCF 4.2 is relatively new.