The code_used_to_analyze_data.pdf file contained in this repository provides the commands and code used to process the VCF files analyzed as part of the manuscript, "Toward a methodology for evaluating DNA variants in nuclear families"
The scripts contained within this repository were executed with the docker container
compound-het-vip.
All scripts except for create_gnomAD_1K_cadd_file.py and keep_passed_variants.py were adapted from
CompoundHetVIP. The
example
here
explains, in detail, how the adapted scripts are used. The publication for
CompoundHetVIP can be found here:
https://doi.org/10.12688/f1000research.26848.2