HPRC-CHM13 PanGenie results

HPRC-CHM13 PanGenie results

Input VCF used for PanGenie for the HPRC experiments based on CHM13, as well as genotyping results, statistics and filters computed. All experiments are based on the Minigraph-Cactus (MC) graph. PanGenie v2.1.1 was used.

Note: PanGenie results for CHM13 provided here are not directly comparable to the GRCh38-based ones provided here: https://doi.org/10.5281/zenodo.6797328. While v1.0.0 was used to produce GRCh38-based results, a newer, more accurate version (v2.1.1) was used to produce the CHM13-based results provided here.

Experiments were run at Heinrich-Heine University Düsseldorf by Jana Ebler ([e-mail]). Pipelines used to produce these results are here: https://github.com/eblerjana/genotyping-pipelines/tree/main/benchmarking-pipeline

How to run PanGenie on the MC variants

We ran PanGenie using the file "chm13_cactus_filtered_ids.vcf.gz" as input (contained in this repository). It was produced from the file "hprc-v1.0-mc-chm13.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 -v chm13_cactus_filtered_ids.vcf -r -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 chm13_cactus_filtered_ids_biallelic.vcf > pangenie_genotyping_biallelic.vcf