Genetics factors associated with resistance to Mtb infection in healthcare workers

What have been done

1. We have joint genotyped the into a combined gVCFS
2. We have annotated the VCFS with VEP to retrieve PolyPhen and SIFT scores as well as GnomAD and 1kg frequecies
3. We have looked into the GenNet package (https://github.com/ArnovanHilten/GenNet) to see if we can train and classify LTBI/Resisters. We were unable to get the data in the correct format so far.

To do
1.Do some comparisons between the two groups LTBI/Resisters for the identified variants for MHC and Clinvar
2.Do some sort of pathway analyse