Simulate reference panel and query haplotypes - Githubissues

szhan / tsimpute

Genome-wide genotype imputation using tree sequences.

MIT License

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Simulate reference panel and query haplotypes #159

Closed szhan closed 10 months ago

szhan commented 10 months ago

Simulation

Simulate a tree sequence with 11k individuals (10k reference + 1k query), each with a 10 Mbp genome.

tsimpute

Reference tree sequence.
Query haplotypes in npy (reference markers).
Query haplotypes in npy (ungenotyped markers masked).

tsinfer + tsimpute

Reference haplotypes in samples file.
Query haplotypes in npy (reference markers).
Query haplotypes in npy (ungenotyped markers masked).

BEAGLE 4.1

Reference haplotypes in VCF.
Query haplotypes in VCF (reference markers).
Query haplotypes in VCF (genotyped markers only).