Thus, we independently intersected intervals L j and R j with the genomic coordinates of all exons of the HSA21 GENCODE v12 annotation by using the intersectBed function of BEDtools (13).
We also noticed a tendency for our highest-scoring intervals to overlap the 56%7474 of 132) of their intervals that intersect genes; our 20 highest scoring intervals overlap 15 of their gene-intersecting intervals, but only three of their intervals that do not intersect any annotated gene.
It is trivial to see that finding maximal valid clusters for all copies of segment ϕ i =(ϕ i ℓ, ϕ i r ) into any position in the genome is equivalent to finding all maximal intersecting breakpoint intervals for all paired-end read mappings ape i.
Two patients have losses with ratios <0.8 intersecting the interval [112101484, 112209836] and seven patients have gains with ratios >1.2 intersecting the same interval.
> -wrap-foot> To address whether the QTL harbor limb-specific polymorphic enhancers, we intersected the intervals with the chromatin mark data reported by Cotney et al. (2012).
We then intersected these intervals with the coordinates of annotated genes to create population-specific lists of candidate genes containing ROHs (see Additional file 1: Table S7 for a list of genes).
To derive the polymorphism densities in different genic regions, we intersected QTL intervals and associated genomic annotations with SNPs at which the parental lines LG/J and SM/J differ.
