Published February 23, 2023
| Version v1
Dataset
Open
Joseph Lalli CHM13-T2T Pangenie reference vcf - unofficial
Description
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.
Files
Files
(6.2 GB)
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md5:bc88c4599c77b16d54adddca45db0472
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1.4 GB | Download |
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md5:08c0b46d005d3d55828e556999aa8d7b
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md5:cb42c1b8bb9b5b459f0186786620dd84
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787 Bytes | Download |
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md5:af90c1df2d389dbe8f7fd2a92472e0aa
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1.5 GB | Download |
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md5:843728951609487215898ed491e2eecf
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958 Bytes | Download |
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md5:8473328b134ccd5f1b46d5f0f1eae9ed
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140.7 MB | Download |
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md5:82dd12f9daa54e3a276cc7dbd390e5dd
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2.1 kB | Download |