The SPB pipeline maps raw reads to a 'flat' version of the GRCh38 reference genome that does not include alternative contigs. The FE pipeline maps reads to the 'full' GRCh38 reference genome, including all alternative contigs. As a result, reads will map differently to each reference genome and the variants from each pipeline are expected to differ (especially in those regions of the 'flat' reference from which the alternative contigs are derived). This BED file provides the coordinates for the ~0.1% of the target regions from which at least one alternative contig is derived.

This resource is not suitable for displaying within a web-browser.
It can be downloaded or viewed using the link: GRCh38_alt_mapping_noCHR.sorted.merged.bed

If you have wget available (typically on linux systems), then you can also obtain a copy using the command

 wget  -nd  biobank.ctsu.ox.ac.uk/ukb/ukb/auxdata/GRCh38_alt_mapping_noCHR.sorted.merged.bed