odelaneau/shapeit4

Issues

• Haploid underflow impossible to recover for [sample]

  #90 opened a month ago by LimKaiShi
  0

• shapeit fails with error message - Segmentation fault (core dumped)

  #45 opened 4 years ago by kvn95ss
  26

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

  #89 opened 8 months ago by hangsuUNC
  0

• Unable to phase chromosome X of a cohort VCF with ~2,000 sample (updated)

  #52 opened 4 years ago by tedyun
  4

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

  #68 opened 3 years ago by klmartinez
  2

• ERROR: Problem opening index file for hg19.fa

  #83 opened 2 years ago by Npaffen
  2

• Reference dataset for Phase 3

  #88 opened a year ago by Anahit19
  0

• error on bingraphsample

  #87 opened 2 years ago by taolincj
  0

• MacOS install error

  #86 opened 2 years ago by jpbreed90
  0

• T2T chromosome maps?

  #85 opened 2 years ago by JosephLalli
  0

• Arch Linux package

  #75 opened 2 years ago by ramiromagno
  1

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

  #81 opened 2 years ago by Shicheng-Guo
  2

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

  #79 opened 3 years ago by pettyalex
  1

• ERROR: Population based phasing for less than 20 individuals

  #77 opened 3 years ago by yaowei2010
  1

• How to handle missing genotype

  #76 opened 3 years ago by rained1989
  1

• Cannot extract map files

  #72 opened 3 years ago by aritra90
  1

• Error: Underflow impossible to recover

  #84 opened 2 years ago by chantisakee
  0

• Pedigree in shapeit4?

  #57 opened 4 years ago by tkn132
  3

• Read-based phasing with underflow error

  #82 opened 2 years ago by Luker121
  0

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

  #80 opened 2 years ago by pettyalex
  0

• Illegal instruction (core dumped)

  #73 opened 3 years ago by Grelot
  3

• SHAPEIT4 compilation error

  #56 opened 4 years ago by lyj95618
  3

• Question about the static HTSlib library dependence

  #74 opened 3 years ago by ramiromagno
  1

• Error: bcf_sr_set_threads was not declared in this scope; did you mean ‘bcf_sr_set_targets

  #53 opened 4 years ago by maojn
  2

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

  #70 opened 3 years ago by xinkaitong
  1

• phasing without imputation

  #69 opened 3 years ago by Shicheng-Guo
  2

• Compilation Issue GCC 5.3.1

  #59 opened 4 years ago by denisemauldin
  2

• Scaffold and WhatsHap (physical and statistical phasing?)

  #71 opened 3 years ago by olekto
  1

• shapeit4.2 - lto1: internal compiler error

  #65 opened 3 years ago by psammarco
  5

• haplotype inference for local region

  #64 opened 3 years ago by Shicheng-Guo
  3

• Getting shapeit4: command not found after successful installation

  #66 opened 3 years ago by rashindrie
  2

• Weird and incorrect behavior when filling missing genotypes

  #61 opened 3 years ago by freeseek
  2

• easy way to estimate required memory

  #63 opened 3 years ago by Shicheng-Guo
  1

• src/utils/otools.h:48:10: fatal error: htslib/hts.h: No such file or directory

  #62 opened 3 years ago by Shicheng-Guo
  0

• Keep old INFO and FORMAT field

  #58 opened 3 years ago by nickhir
  1

• Core dump on invoking on CentOS8

  #60 opened 3 years ago by brucedesertrat
  1

• Unable to install with conda

  #55 opened 4 years ago by tkn132
  1

• free(): invalid pointer \n Aborted (core dumped)

  #54 opened 4 years ago by Bennouhan
  2

• Unable to phase chromosome X of a cohort VCF with ~2,000 sample

  #51 opened 4 years ago by tedyun
  1

• ERROR: Parsing line 0 : incorrect number of columns, observed: 1 expected: 3

  #50 opened 4 years ago by jessicahr
  2

• build issue in docker Unbuntu 20.04

  #49 opened 4 years ago
  3

• Buffer read overflow in pbwt_solver::sweep

  #47 opened 4 years ago by cnettel
  0

• '--pbwt-disable-init' not recognized

  #46 opened 4 years ago by mvaudel
  2

• About including PS (phase set) information

  #42 opened 4 years ago by SIJAE-WOO
  2

• Question on recombination maps

  #44 opened 4 years ago by BJWiley233
  2

• Question in test folder hapmap for b37 chr20

  #43 opened 4 years ago by BJWiley233
  2

• Segmentation fault (core dumped)

  #41 opened 4 years ago by SIJAE-WOO
  1

• whatshap phase set variants

  #39 opened 4 years ago by Ahhgust
  3

• missing genotypes in scaffold

  #40 opened 4 years ago by 23andme-jaredo
  2

• core dumped at genotype_reader2.cpp:127

  #38 opened 4 years ago by verne91
  1