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thread

thread is a software package for reconstructing ancestral genomes, given a pedigree structure and genotype data from recent individuals. See our preprint for more details about the method. Before using thread, genotype or sequence data should be phased (recommended: SHAPEIT2) and then IBD segments should be called (recommended: GERMLINE). Then thread can be applied using two steps:

  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.

We have implemented two different algorithms for selecting the source of each IBD segment ("min path" and "max prob"). "min path" is the default. To use "max prob" instead, use the -x flag:

$ 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 -x

To create reproducible results, use the PYTHONHASHSEED. For example:

$ PYTHONHASHSEED=42 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

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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Ancestral haplotype reconstruction using pedigrees

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