VCF modifications before plink analysis

Question

[hrora]

Hi everyone, I am adding new vcf files to a previously made bcf file in which the ID field in the VCF had been set to CHR:POS:POS:REF:ALT ? How do I set the ID field in the VCF to CHR:POS:POS:REF:ALT ?

Thanks

Answer 1

[Kevin Blighe]

Hey hrora,

You can set the VCF ID field to CHR:POS:POS:REF:ALT with:

bcftools annotate -Ob -x 'ID' -I +'%CHROM:%POS:%POS:%REF:%ALT' MyVCF.vcf > out.bcf ;

To output VCF, use -Ov, not -Ob.

May I also recommend that you normalise your VCF by splitting multi-alleles into separate records and also left-aligning indels with the following piped commands:

bcftools norm -m-any MyVCF.vcf | \
bcftools norm --check-ref w -f human_g1k_v37.fasta | \
bcftools annotate -Ob -x 'ID' -I +'%CHROM:%POS:%POS:%REF:%ALT' > out.bcf ;

The middle command requires a reference genome - this is for left-aligning indels. If it's not needed, then simply remove that middle command.

Kevin