Combining two VCFs each with own set of mutations

Question

[vctrm67]

I have two VCF files, each containing somatic mutation calls on each chromosome (ie. the VCFs are not separated by chromosome number or mutation position - they each contain calls on every chromosome) . I want to combine these two files into one. What is the best tool to do this? I tried bedtools concat but I get this message:

Different number of samples in /path/to/vcf. Perhaps "bcftools merge" is what you are looking for?
[W::bcf_hdr_merge] Trying to combine "AD" tag definitions of different lengths

Should I be using the merge function?

Answer 1

[jared.andrews07]

bcftools merge is likely what you want. It will preserve the VCF format and genotype information for each sample appropriately.

[vctrm67]

They should be from the same sample. Does this make a difference?

To provide some clarification, these are VCFs that contain calls made by two different callers on the same sample. I want to combine them into one VCF and annotate that.

[jared.andrews07]

That's fine, it can still merge them and will even help you determine which caller called which variant (or where they overlap).