Question: Combining two VCFs each with own set of mutations
0
gravatar for vctrm67
11 months ago by
vctrm6710
vctrm6710 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 • 381 views
ADD COMMENTlink modified 11 months ago by jared.andrews077.1k • written 11 months ago by vctrm6710
0
gravatar for jared.andrews07
11 months ago by
jared.andrews077.1k
Memphis, TN
jared.andrews077.1k wrote:

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

ADD COMMENTlink written 11 months ago by jared.andrews077.1k

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 REPLYlink written 11 months ago by vctrm6710

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

ADD REPLYlink written 11 months ago by jared.andrews077.1k
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