phasing_genotyping

common variant phasing (MAF >=0.1%) and rare variants (MAF<0.1%)

Singleton phasing(singleton variants (minor allele count (MAC) of 1))

This is a well-known limitation of all statistical phasing methods. SHAPEIT5 can provide inference at these sites by using the Viterbi algorithm for the Li and Stephens model, to obtain the longest shared IBD segment between each one of the two target haplotypes and the conditioning haplotypes.

SHAPEIT5: https://odelaneau.github.io/shapeit5/

Hofmeister R J, Ribeiro D M, Rubinacci S, et al. Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank[J]. Nature Genetics, 2023, 55(7): 1243-1249.

The pipeline uses BCFtools for marker filtering, Beagle for genotype phasing, and Tabix for VCF indexing.The pipeline’s QC filter excludes markers with AAScore <=0.95, markers with >=5% missing data, and non-SNV markers.

ukb-phasing:https://github.com/browning-lab/ukb-phasing/

Browning B L, Browning S R. Statistical phasing of 150,119 sequenced genomes in the UK Biobank[J]. The American Journal of Human Genetics, 2023, 110(1): 161-165.

graphtyper

Eggertsson H P, Jonsson H, Kristmundsdottir S, et al. Graphtyper enables population-scale genotyping using pangenome graphs[J]. Nature genetics, 2017, 49(11): 1654-1660.

Eggertsson H P, Kristmundsdottir S, Beyter D, et al. GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs[J]. Nature communications, 2019, 10(1): 5402.