Issues

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

  odelaneau/shapeit4#92 · Filter by author wanyi0309 opened on May 8, 2026

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

  odelaneau/shapeit4#91 · Filter by author ReynaDeR opened on May 4, 2026

• Haploid underflow impossible to recover for [sample]

  odelaneau/shapeit4#90 · Filter by author LimKaiShi opened on Nov 29, 2024

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

  odelaneau/shapeit4#89 · Filter by author hangsuUNC opened on May 6, 2024

• Reference dataset for Phase 3

  odelaneau/shapeit4#88 · Filter by author Anahit19 opened on Jul 12, 2023

• MacOS install error

  odelaneau/shapeit4#86 · Filter by author jpbreed90 opened on Feb 25, 2023

• T2T chromosome maps?

  odelaneau/shapeit4#85 · Filter by author JosephLalli opened on Jan 24, 2023

• Error: Underflow impossible to recover

  odelaneau/shapeit4#84 · Filter by author chantisakee opened on Oct 31, 2022

• ERROR: Problem opening index file for hg19.fa

  odelaneau/shapeit4#83 · Filter by author Npaffen opened on Oct 20, 2022
  2

• Read-based phasing with underflow error

  odelaneau/shapeit4#82 · Filter by author Luker121 opened on Jul 27, 2022

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

  odelaneau/shapeit4#81 · Filter by author Shicheng-Guo opened on Jul 8, 2022
  2

• AVX2 usage is determined at compile-time, not runtime

  odelaneau/shapeit4#80 · Filter by author pettyalex opened on Jul 7, 2022

• Reading in files and genetic maps is done sequentially, and could be parallelized across threads

  odelaneau/shapeit4#79 · Filter by author pettyalex opened on Jul 6, 2022
  1

• ERROR: Population based phasing for less than 20 individuals

  odelaneau/shapeit4#77 · Filter by author yaowei2010 opened on Jun 9, 2022
  1

• How to handle missing genotype

  odelaneau/shapeit4#76 · Filter by author rained1989 opened on Jun 8, 2022
  1

• Illegal instruction (core dumped)

  odelaneau/shapeit4#73 · Filter by author Grelot opened on Feb 24, 2022
  3

• Cannot extract map files

  odelaneau/shapeit4#72 · Filter by author aritra90 opened on Feb 8, 2022
  1

• Scaffold and WhatsHap (physical and statistical phasing?)

  odelaneau/shapeit4#71 · Filter by author olekto opened on Nov 6, 2021
  1

• how to reduce the RAM when phasing a large cohort (~1200) of whole genome sequencing data with about 10Mb?

  odelaneau/shapeit4#70 · Filter by author xinkaitong opened on Oct 29, 2021
  1

• phasing without imputation

  odelaneau/shapeit4#69 · Filter by author Shicheng-Guo opened on Oct 22, 2021
  2

• Losing ~60% of variants from sequence data with SHAPEIT

  odelaneau/shapeit4#68 · Filter by author klmartinez opened on Sep 27, 2021
  2

• shapeit4.2 - lto1: internal compiler error

  odelaneau/shapeit4#65 · Filter by author psammarco opened on Sep 15, 2021
  5

• haplotype inference for local region

  odelaneau/shapeit4#64 · Filter by author Shicheng-Guo opened on Sep 13, 2021
  3

• easy way to estimate required memory

  odelaneau/shapeit4#63 · Filter by author Shicheng-Guo opened on Sep 10, 2021
  1

• Weird and incorrect behavior when filling missing genotypes

  odelaneau/shapeit4#61 · Filter by author freeseek opened on Jul 23, 2021
  2