[TODO] 1KG population reference

[yk-tanigawa]

• 1000 Genome reference panel has an advantage that they have phased information
• [TODO]
  • Prepare 1KG population reference (pgen)
  • Compute prior probability of haplotype (population frequency)
  • Compute posterior probability given data

[yk-tanigawa]

[done] pgen file preparation

• decided to use --make-bpgen option of plink2 instead of --make-pgen option
  • --make-bpgen is pgen + bim + fam
  • it looked easy to work with bim instad of pvar
• https://github.com/rivas-lab/nanopore/blob/25fcf60c0d5eb4f0aa415cae6cfd382dd8bd2369/dev/scripts/20170209/1KG_vcf2pgen.12703239.sh

[yk-tanigawa]

prior distribution of haplotype given a mapped fragment

• wrote a code to query pgen file and obtain prior distribution of haplotype in the population.
  • at this moment, we just simply define haplotype as a phased genotypes for a region on the genome given mapped fragment
• I tried on the first example on chromosome 20, but turned out that 1KG population reference has only 1 haplotype.
  • https://github.com/rivas-lab/nanopore/blob/7f071514def7059f99e18808886626600851c040/dev/scripts/20170209/20170209_haplotype_prior.ipynb

[yk-tanigawa]

Bayesian_online_inference_of_haplotype

• 1KG has 225 haplotypes in 32 kb region on chromosome 20 for a given mapped fragment
  • the fragment has 15 SNPs on this region
• prior probability of the haplotype is determined by population frequency
• posterior probability can be found by binomial likelihood

prior distribution

posterior distribution

note

• https://github.com/rivas-lab/nanopore/blob/feab7e509fc05b79591d283ae24554764dc64c90/dev/scripts/20170210/20170210_Bayesian_online_inference_of_haplotype.ipynb