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Inconsistent SHAPEIT4 Phasing Outcomes Using Full vs Phased-Heterozygous-Only VCF Inputs

Status: Open.

#92 In odelaneau/shapeit4;

· wanyi0309 opened on May 8, 2026

Would the genetic map files in from shapeit4 be useful for those in shapeit5?

Status: Open.

#91 In odelaneau/shapeit4;

· ReynaDeR opened on May 4, 2026

Haploid underflow impossible to recover for [sample]

Status: Open.

#90 In odelaneau/shapeit4;

· LimKaiShi opened on Nov 29, 2024

Error:[31mERROR: [0mCould not find conditioning haplotypes for [1032052] / check options --pbwt-* and --ibd2-*

Status: Open.

#89 In odelaneau/shapeit4;

· hangsuUNC opened on May 6, 2024

Reference dataset for Phase 3

Status: Open.

#88 In odelaneau/shapeit4;

· Anahit19 opened on Jul 12, 2023

MacOS install error

Status: Open.

#86 In odelaneau/shapeit4;

· jpbreed90 opened on Feb 25, 2023

T2T chromosome maps?

Status: Open.

#85 In odelaneau/shapeit4;

· JosephLalli opened on Jan 24, 2023

Error: Underflow impossible to recover

Status: Open.

#84 In odelaneau/shapeit4;

· chantisakee opened on Oct 31, 2022

ERROR: Problem opening index file for hg19.fa

Status: Open.

#83 In odelaneau/shapeit4;

· Npaffen opened on Oct 20, 2022

Read-based phasing with underflow error

Status: Open.

#82 In odelaneau/shapeit4;

· Luker121 opened on Jul 27, 2022

Indel, CNV and Structural Variation (SV) in Shapeit4 phasing analysis

Status: Open.

#81 In odelaneau/shapeit4;

· Shicheng-Guo opened on Jul 8, 2022

AVX2 usage is determined at compile-time, not runtime

Status: Open.

#80 In odelaneau/shapeit4;

· pettyalex opened on Jul 7, 2022