Convert vcf files with phased genotypes to standard haplotype format

Question

[Mr Locuace]

Hello, I have a set of .vcf files with phased genotypes that I would like to convert to standard haplotype format (.hap). Is there any tool that makes this?

Here is a toy example of a .hap file of a population of 2 human individuals, with 12 SNPs each:

1  1 2 2 1 2 2 2 1 1 1 1 1
2  1 1 1 2 1 1 2 2 1 2 1 2
3  1 1 2 1 2 2 1 1 2 2 1 2 
4  2 2 2 2 2 2 1 1 1 1 1 1

Each line represents a chromosome, the first element being the haplotype ID. 1 and 2 represent ancestral and derived alleles, respectively.

Many thanks

Answer 1

[chrchang523]

Assuming all of your genotypes are phased, this should be doable with recent plink 2.0 alpha builds (which you can download from https://www.cog-genomics.org/plink/2.0/ ):

plink2 --vcf phased.vcf --export haps --out new_filename_prefix

[Mr Locuace]

Thank you for your help @chrchang523 !. The solution you provide outputs minor/major alleles (0/1) but not ancestral/derived alleles. Do you know how can I get the latter coded as 0/1?. Thanks again

[chrchang523]

plink2 codes the REF allele as 1 and the ALT allele as 0 in the .haps file. If they don't always correspond to the ancestral/derived allele distinction you want, you can use --ref-allele or --alt1-allele (https://www.cog-genomics.org/plink/2.0/data#ref_allele ) to swap them around when necessary (you'll need to create a tab-delimited table with all the variant IDs and ancestral/derived alleles).

[shrutishreyajha]

Hi, I am encountering the same problem with my VCF files and hap files creation with Ancestral/Derived Allele. I need that for running rehh package. Was your problem solved?