An Icelandic pangenome reference (HPRC-ICE)

HPRC-ICE An Icelandic pangenome reference built from HPRC samples, GRCh38, T2T-CHM13 and 698 Icelandic haplotype assemblies. The Icelandic haplotype assemblies (aliased with ICE0001, ICE0002, etc) are mosaic, constructed from many random shuffles of haplotype sequences, to ensure strict privacy. The three main files are `HPRC-ICE.gfa.gz` (graph), `HPRC-ICE.vcf.gz` (haplotypes) and `HPRC-ICE.gfa.alts` (segments/SVs that are very common/HPRC AF>10%). Other files are constructed from those three and can be generated to limit amount of downloaded data (see details below). Usage Short reads can be mapped to HPRC-ICE using weaver I.e. weaver map HPRC-ICE.gfa <reads.fq[.gz]> | samtools markdup -u - - | samtools view --remove-tag ms -b -o final.bamsamtools index final.bam You can also use the weaver Nextflow workflow if you prefer. The read alignments are represented in context of the stable sequences of the graph in `HPRC-ICE.fa`. Load that reference in your read alignment visulization tool (IGV, samtools tview, ...) when inspecting output and when subsequently variant calling.