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).
- Produce a
jsonfile (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
- Run the reconstruction pipeline, optionally producing a
pedfile 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