HPRC-CHM13 PanGenie results

<p><strong>HPRC-CHM13 PanGenie results</strong></p> <p>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.</p> <p><strong>Note:</strong> PanGenie results for CHM13 provided here are <strong>not</strong> directly comparable to the GRCh38-based ones provided here: <a href="http://doi.org/10.5281/zenodo.6797328">https://doi.org/10.5281/zenodo.6797328</a>. 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.</p> <p>Experiments were run at Heinrich-Heine University D&uuml;sseldorf by Jana Ebler (ebler@hhu.de). Pipelines used to produce these results are here: <a href="/github.com/eblerjana/genotyping-pipelines/tree/main/benchmarking-pipeline">https://github.com/eblerjana/genotyping-pipelines/tree/main/benchmarking-pipeline</a></p> <p>&nbsp;</p> <p><strong>How to run PanGenie on the MC variants</strong></p> <p>We ran PanGenie using the file &quot;chm13_cactus_filtered_ids.vcf.gz&quot; as input (contained in this repository). It was produced from the file &quot;hprc-v1.0-mc-chm13.vcf.gz&quot; 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: <a href="https://bitbucket.org/jana_ebler/hprc-experiments/src/master/genotyping-experiments/workflow/scripts/convert-to-biallelic.py">https://bitbucket.org/jana_ebler/hprc-experiments/src/master/genotyping-experiments/workflow/scripts/convert-to-biallelic.py</a></p> <pre><code># run PanGenie, produces genotyped VCF "pangenie_genotyping.vcf" PanGenie -i &lt;input-reads&gt; -v chm13_cactus_filtered_ids.vcf -r &lt;reference-genome&gt; -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 &gt; pangenie_genotyping_biallelic.vcf</code></pre> <p>&nbsp;</p> <p>&nbsp;</p>