GERP scores lifted from ARS1 over the novel Capra Ibex reference genome (CapIbe1.0)

Whole-genome alignment between Capra ibex (CapIbe1.0) and Capra hircus (ARS1) was performed using minimap2 (v2.24) with the asm5 preset. The resulting PAF file was converted to a chain file using paf2chain. Conservation scores in BigWig format for C. hircus ARS1 genome were converted to BedGraph using bigWigToBedGraph. The chain file was used to lift over the conservation scores from C. hircus to C. ibex coordinates using UCSC's liftOver tool. The lifted BedGraph file was sorted with bedops sort-bed, and overlapping intervals —potentially introduced during liftover— were resolved by partitioning and averaging scores using bedops and bedmap. The final BedGraph file was then converted to BigWig format using bedGraphToBigWig.