Add AF from 1000 genomes vcf file to a different vcf file

Question

[GK1610]

I have a my_vcf file containing genotypes of 600 individuals. These individuals are from European descent.

I want to use AF from 1000 genomes phase 3 project of European population.

I have subsetted 100 genomes phase3 vcf file for European population using following command.

vcf-subset -c EUR.samples.list ALL.chr13.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz | fill-an-ac | bgzip -c > EUR.chr13.phase1.vcf.gz

I want to add these Allele frequencies from here to my original my_vcf file.

How do I do this?

Answer 1

[trausch]

bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF <input.bcf>

[GK1610]

Thanks. its working.

[GK1610]

Thanks. I got this working. Now I am having trouble with editing the vcf file. which means

bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/EUR_AF my_vcf > EUR_AF.vcf

Now I want to replace EUR_AF with AF and also edit this in the header of the file.

[trausch]

bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF:=INFO/EUR_AF my_vcf > EUR_AF.vcf

Answer 2

[finswimmer]

Hello,

SnpSift can do this for you.

 $ java -jar SnpSift.jar annotate -info AF EUR.chr13.phase1.vcf.gz my_vcf.vcf > variants_annotated.vcf

You have to set the value of -info to what ever is used in your EUR.chr13.phase1.vcf.gz.

Add a -noId if you don't want SnpSift to annotate the ID column as well.

fin swimmer