Mutation caller tools: MutationCaller3.py Current draft of the mutation caller script. In a future update, I will make the setup.py file so that it can handle its own dependencies, but for the moment, it requires the following dependencies: -PyVCF3 (It now uses a modified version I altered, I will figure out a way to make this available) --(not to be confused with PyVCF, which is not being supported anymore and is complicated to get functioning for python3.) --I will be replacing this with my own modified package when I succeed in getting programs to correctly import and interpret it. It is already written, it is currently called PyVCF3_mod, but is not currently being found -collections -multiprocessing -concurrent.futures -functools -sys -numpy -unittest
Utility tools:
double_seg_sorter.sh: Converts a HapIBD IBD segment output format to the pair of sorted IBD segment files required by our mutation caller.
Test Input Files for experimentation: (The main testing file I use is too large for github, I will create a functional, smaller version to upload)
segsTest1.seg -A basic HapIBD format file for ibd segment input
TestInput.vcf.gz -A smaller test vcf. Formatting may not be viable as of most recent update, and is not used in any current test.
testPedigree1.ped -example pedigree input file