Entering edit mode
4.5 years ago
vctrm67
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50
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?
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.
That's fine, it can still merge them and will even help you determine which caller called which variant (or where they overlap).