Joseph Lalli CHM13-T2T Pangenie reference vcf - unofficial

hprc-jun1-mc-chm13.pangenie_panel.bcf.gz: Draft pangenome (Jun1-mc version) in CHM13-T2T coordinates hprc-jun1-mc-chm13.fasta: CHM13 reference paths from Jun1-mc draft pangenome. hprc-jun1-mc-chm13.fasta.fai: Reference index. pangenie.def and pangenie.sif: Singularity container to run Pangenie 2.1 run_pangenie.sh: Bash script to run pangenie on HTCondor servers. Specifically, the script downloads a specified 1KGP unaligned cram file, extracts the reads locally, creates a checkpoint .jf kmer count table, and then runs Pangenie on the .jf file. The resulting vcf file is compressed to a bcf.gz file, and is saved in the staging directory. HG02030.pangenie.bcf.gz: An example of the output from the 1KGP sample HG02030.