README.md

User sites

Use the template in this folder to add additional STR sites to the TREDPARSE run. By default, in addition to the 30 standard STR loci, TREDPARSE also look for JSON files in sites in the current working directory.

Most of the details can be manually filled out, however, the prefix and suffix fields need to be computed from the reference FASTA. Therefore we've included a script to extract such sequences.

Example

Initiate a template by the following command:

python tredprepare.py

The scripts does a questionaired similar to the following:

Enter the locus name [HD]: PIEZO1
Sequence motif [CAG]: TCC
Number of motifs in reference [19]: 8
Chromosomal start location (1-based) [chr4:3074877]: chr16:88733965
Enter the FASTA path [/mnt/ref/hg38.upper.fa]:
AGCCCCTCGTCCCTGGAG|tcctcctcctcctcctcctcctcc|TGCTGCTGCTGCTGATGC

Template json file is written to `sites/PIEZO1.json`
Please manually fill in the remaining details

The user will then need to modify the generated sites/*.json to fill in additional information - most critically, the cutoff_risk and inheritance. Please see the include PIEZO1.json for a sample JSON file.