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Haplotype sampling (-x option)

Status: Open.

#102 In eblerjana/pangenie;

· laflamro opened on Jul 9, 2025

Phasing of variants VCF file from PGGB

Status: Open.

#101 In eblerjana/pangenie;

· aamirwkhan06 opened on Jun 17, 2025

Inquiry About Incorporating a Haploid Genome into Pangenie Pangenome

Status: Open.

#96 In eblerjana/pangenie;

· HuangYihang1222 opened on Apr 3, 2025

Issue with Generating VCF for PanGenie Using the Pipeline

Status: Open.

#95 In eblerjana/pangenie;

· HuangYihang1222 opened on Feb 26, 2025

issue in Create PanGenie-ready VCF from Minigraph-Cactus VCF

Status: Open.

#94 In eblerjana/pangenie;

· ChuanzhengWei opened on Feb 17, 2025

No heterozygous missing genotypes?

Status: Open.

#93 In eblerjana/pangenie;

· dmjask opened on Jan 22, 2025

Haploid Haplotype Reconstruction

Status: Open.

#88 In eblerjana/pangenie;

· gsc74 opened on Sep 24, 2024

Wrong kmer abundance peak

Status: Open.

#86 In eblerjana/pangenie;

· baozg opened on Aug 29, 2024

lower SNP overlap rate between call set and GATK results.

Status: Open.

#76 In eblerjana/pangenie;

· ttian627 opened on May 24, 2024

How to handle N bases in VCF-input files

Status: Open.

#75 In eblerjana/pangenie;

· isaamael opened on Apr 23, 2024

pangenome-graph-from-assemblies not working for latest Pangenie

Status: Open.

#73 In eblerjana/pangenie;

· LYC-vio opened on Apr 15, 2024

since alleles contain undefined nucleotides

Status: Open.

#72 In eblerjana/pangenie;

· jwli-code opened on Apr 1, 2024