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Question: Combining two VCFs each with own set of mutations
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gravatar for vctrm67
4 months ago by
vctrm67 • 10
vctrm67 • 10 wrote:

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?
vcf • 171 views
ADD COMMENT • link •
modified 4 months ago by jared.andrews07 ♦ 4.9k • written 4 months ago by vctrm67 • 10
0
gravatar for jared.andrews07
4 months ago by
jared.andrews07 ♦ 4.9k
St. Louis, MO
jared.andrews07 ♦ 4.9k wrote:

bcftools merge is likely what you want. It will preserve the VCF format and genotype information for each sample appropriately.
ADD COMMENT • link written 4 months ago by jared.andrews07 ♦ 4.9k

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.

ADD REPLY • link written 4 months ago by vctrm67 • 10

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

ADD REPLY • link written 4 months ago by jared.andrews07 ♦ 4.9k
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