This is the ATaRVa analysis repository, which contains Python scripts for calculating Mendelian inheritance from trio samples, measuring tandem repeat allele lengths from assemblies, and a Jupyter notebook for computing allele length concordance using VCFs generated by ATaRVa and other tools such as TRGT, LongTR, Medaka Tandem, STRkit, Straglr, TREAT and GangSTR.

For concordance calculation, first generate the maternal and paternal assembly_allele.bed files using aam.py. These files will be used to compare and calculate each tool's concordance. Please refer to the README.md files in the respective folders for detailed instructions.