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Ancestral haplotype reconstruction using pedigrees
Python
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example
AncestorNode.py
Couple.py
IBD.py
IBD_Group.py
IBD_content.py
Individual.py
PedigreeTree.py
README.md
Reconstruction.py
match2json.py
probabilities.py
recombination_points.py
thread.py
util.py

README.md

thread

thread is a software package for reconstructing ancestral genomes, given a pedigree structure and genotype data from recent individuals. Genotype or sequence data should be phased (recommended: SHAPEIT2) and then IBD segments should be called (recommended: GERMLINE).

  1. Produce a json file (creates a dictionary to hold IBD information from GERMLINE):
$ python3 match2json.py -g example/toy_germline.match -s example/toy_pedigree.txt -m example/toy.map -p example/toy_geno.ped -j example/toy.json
  1. Run the reconstruction pipeline, optionally producing a ped file of sequence information for the reconstructed individuals:
$ python3 thread.py -g example/toy_germline.match -s example/toy_pedigree.txt -m example/toy.map -j example/toy.json -p example/recon.ped

This recon.ped file can be compared with the true ancestral haplotypes (known in this simulated) example: toy_anc.ped.

Note that this software is under active development. Please contact Sara Mathieson (smathieson [at] haverford [dot] edu) with any questions.

Contributors:

  • Kelly Finke kellyfinke
  • Michael Kourakos mkourak1 / MikeyManiac
  • Gabriela Brown gabcbrown
  • Sara Mathieson saramathieson
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