The PMS2 gene and PMS2CL pseudogene are located on chromosome 7.
Paraphase differentiates the gene from pseudogene based on whether the haplotype extends beyond the homology region into the unique region.
Fields shared across all genes are defined in the general json file. The PMS2 locus does not include unique fields.
The PMS2 haplotypes are labeled pms2_pms2hap# and pseudogene pms2_pms2clhap#.
To visualize phased haplotypes, load the output bam file in IGV, group reads by the HP tag and color alignments by YC tag. Reads are realigned to PMS2.
Reads in blue are confidently consistent with a single haplotype. Reads in gray are either unassigned or consistent with more than one possible haplotype. When two haplotypes are identical over a region, there can be more than one haplotype consistent with a read, and the read is randomly assigned to a haplotype and colored in gray.
