Benchmarking datasets for Haplotype phasing
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2.8 years ago
kirannbishwa01 ★ 1.3k

I have been trying to run a benchmark test on one the haplotype phasing application. I tried to navigate around to find tutorials for it and found this to be a good one: https://portal.biohpc.swmed.edu/content/training/bioinformatics-nanocourses/gwas/zhan-phasing-workshop/

I like this tutorial because it is simple and straight forward. The haplotype database I am trying to use is from CEU (NA12891) which is considered a gold standard. I am able to find the NA12891 database in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/ but still can't narrow down the same exact database.


These are the data I am looking for :

  • hapmap3_r2_b36_chr20.haps (HAPS file)
  • all.sample (SAMPLE file)
  • hapmap3_r2_b36_chr20.legend (LEGEND file)
  • genetic_map_chr20_combined_b36.txt (Genetic map file)
genome haplotype phasing shapeit NA12891 • 798 views
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