HPRC PanGenie results

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 ([email protected]). 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