HPRC PanGenie results Input VCF used for PanGenie for the HPRC experiments as well as genotyping results, statistics and filters computed. All experiments are based on the Minigraph-Cactus (MC) graph. Experiments were run at Heinrich-Heine University Düsseldorf by Jana Ebler (ebler@hhu.de). Pipelines used to produce these results are here: http://bitbucket.org/jana_ebler/hprc-experiments/src/master/genotyping-experiments/ How to run PanGenie on the MC variants We ran PanGenie using the file "cactus_filtered_ids.vcf.gz" as input (contained in this repository). It was produced from the file "hprc-v1.0-mc-grch38.vcf.gz" generated from the MC graph using vg decompose. The output VCF generated by PanGenie can be converted into a bi-allelic VCF containing a single record for each (nested) variant allele, i.e. after decomposing large bubbles into their nested variants using the script: https://bitbucket.org/jana_ebler/hprc-experiments/src/master/genotyping-experiments/workflow/scripts/convert-to-biallelic.py # run PanGenie, produces genotyped VCF "pangenie_genotyping.vcf" PanGenie -i <input-reads> -v cactus_filtered_ids.vcf -r <reference-genome> -o pangenie -j 24 -t 24 # decompose bubbles and produce a bi-allelic VCF with genotypes for each (nested) allele cat pangenie_genotyping.vcf | python3 convert-to-biallelic.py cactus_filtered_ids_biallelic.vcf > pangenie_genotyping_biallelic.vcf