from phased SNPs to haplotype blocks (or phase sets)

Question

[Nicola Casiraghi]

Hi all, I have successfully phased a set of heterozygous SNPs (only one sample) via the EAGLE2 phasing-only pipeline provided by the Sanger Imputation Server.

Specifically, the output that I got from the pipeline contains ~90% of the total number of the input SNPs and the output contains only SNPs with phased information 0|1 or 1|0.

I am now interested in define haplotype blocks accordingly with computed phase information. Usually, in a VCF file, haplotype blocks (or phase sets) have a unique identifier, which is attached to a genotype using the PS tag. The VCF output from EAGLE2 does not have the PS tag.

How can I group together phased SNPs belonging to the same haplotype block without having the PS tag?

thanks a lot for the help

Answer 1

[Peter Chung]

maybe HAPCUT2 ?

./build/HAPCUT2 --fragments fragment_file --VCF variants.vcf --output haplotype_output_file

it gives you the haplotype blocks output file