STRdiff is a project-specific tool for inferring the parent-of-origin for de novo STR mutations found in the CEPH pedigrees.
De novo STR mutations are first identified in the CEPH parents using a tool like HipSTR.
The program infers chromosomal phase in the trio containing the parent with the de novo STR and the grandparents. The rest of the family is also phased independently. The new STR allele is identified on the phased chromosomes in the children. Because phased WGS data can contain genotyping errors, phasing issues, new SNP mutations, and rare variants, a consensus chromosome carrying the de novo STR allele created. This consensus is then compared to phased chromosome in the grandparents of the parent with the de novo STR allele to identify the most likely grandparental chromosome transmitting the de novo allele. The size difference between the original and de novo allele is determined using information in the vcf file.
