How to add reference as new sample to vcf?

Question

[沛煒]

Hello,

Do anyone know how to make a vcf file with a new sample from reference genome?

I have a vcf file with 200 samples and 2,000 SNP

My SNP were called with a reference genome, and I want to add the retained SNP of my reference as a new sample to my vcf file

I know that I only have the haploid reference genome, so I like to write all retained loci from the reference as homozygote in the new vcf file

Thanks for any suggestion or solution!

[Pierre Lindenbaum]

please define the retained SNP of my reference

[沛煒]

After SNP calling and filtering, I kept 2,000 SNP, and these SNPs are the retained SNP I also want to keep from the reference genome

[Pierre Lindenbaum]

I want to add the retained SNP of my reference as a new sample to my vcf file

what should be the genotype for the new SAMPLE ? say, there is a sample 1/0 and another is 1/1 and another is ./.

[沛煒]

For the new sample, all genotypes should be 0/0

Answer 1

[Colaptes]

Here is an awk script, add_reference.awk that I wrote for this task. It adds a new sample called "Reference" that will be homozygous 0/0 at each locus.

#! /usr/bin/awk -f 

BEGIN {
    FS = "\t"
    OFS = FS
}

#print the header info as-is
/^##/ {
    print
    next
}

#add sample named "Reference" to the list of samples
/^#CHROM/ {
    print $0"\tReference"
    next
}

#add homozygous reference allele to every locus.
{
    print $0"\t0/0:0,0,255:100:0:100,0:1,0,0:150"
}

For gzipped VCF files, I run it like this:

zcat my_file.vcf.gz | add_reference.awk | bgzip > my_file_with_reference.vcf.gz 

You will probably have to change it to match the format of your VCF. My fields are in the format "GT:PL:DP:SP:AD:GP:GQ" so I went with an entry of "0/0:0,0,255:100:0:100,0:1,0,0:150" so that it would pass my downstream filters, but you can change it to match whatever fields you have in your VCF.

It assumes that all loci are unphased diploid loci and that the reference sample is not heterozygous at any site. Caveat: ignoring heterozygous sites in the ref sample may cause inaccuracies in certain downstream analyses depending on what it is used for.