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Combining vcf files so that same loci data is combined

I have vcf files that I wish to combine so that any variants with matching positions are combined also. For example, if I have a variant in one file at position 123 and also one in another file there, I want that information to be combined in the genotype info.

The actual variants will be the same (T->G in one file will always be T->G in the other) as they have been created using the same reference data.

Is this possible to do in one go with any tool?

snp
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updated by nosavax245 • nosavax245 • written by spiral01 spiral01

2 answers

Is each file a different sample? If so, it sounds like GATK's CombineVariants tool would fit your purpose.

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written by jared.andrews07 jared.andrews07

Thanks for your reply. Yes each file is a single individual. I am trying to combine the vindija and altai neanderthal vcf data. Both have been created using the hg19 as reference and I just want to combine the two vcf files in one.

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written by spiral01 spiral01

I think that should do the trick for you then. Let me know if you have any issues.

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written by jared.andrews07 jared.andrews07

You'll want to download the hg19.2bit file and then use their utility to convert it to a Fasta file.

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written by jared.andrews07 jared.andrews07

Whilst Jared's answer above worked perfectly, I also had success using bcftools merge with the --force-samples argument.

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written by spiral01 spiral01

Go ahead and accept (green check mark) your and @Jared's answer to provide closure to this thread.

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written by GenoMax GenoMax

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