JBrowseMar 5, 2025
Colin D

finally made a little breakthrough on finding "phased segments" from a phased VCF...had to twiddle with the hap-ibd settings to lower the defaults to output much smaller blocks. these are fragmented, but do correspond to valid blocks from what i can tell

picture shows the correspondence between hap-ibd output and the raw VCF data with a trio VCF (6 rows, each row being a haplotype of the sample)

Mar 5, 2025 at 4:00amWeb
Show threadColin DMar 5, 2025

I realized this picture is actually a beautiful depiction of crossing-over recombination.

From Bio101, we know crossing-over occurs during meiosis during the production of gametes, so the mom has a crossing over event and the dad has a crossing over event right here

This leads to a continuous stretch of the child matching two haplotypes from mom, and two haplotypes from dad right in this area