odelaneau/shapeit5

Issues

• No static binaries for Linux/RHEL found in the download links

  #110 opened 3 months ago by Toseph
  0

• phase_common sometimes creates Mendelian errors for missing genotypes when phasing with --pedigree

  #109 opened 3 months ago by kkellysci
  0

• ligate won't treat offspring as scaffolded unless parents are still in data

  #108 opened 3 months ago by kkellysci
  0

• where to find binaries

  #107 opened 4 months ago by js134711
  1

• [QUESTION] Partially phased VCF as input

  #106 opened 4 months ago by davidyuyuan
  0

• Feature request: VCF output

  #105 opened 4 months ago by pettyalex
  0

• phase_common failing at PBWT step

  #96 opened 8 months ago by nmshahir
  2

• file extention not recognized

  #65 opened a year ago by marlmatos
  8

• Phasing small sample sizes

  #85 opened a year ago by sihaybo
  3

• Columns for .flipsAndSwitches.txt.gz

  #70 opened a year ago by karinkumar
  1

• about merging multiallelics

  #104 opened 5 months ago by vicbp1
  0

• Segmentation fault when using genetic map

  #101 opened 6 months ago by GenevieveKrause
  2

• Can only run a few base positions on chromosome X

  #102 opened 6 months ago by milena-andreuzo
  3

• vcf_to_sparse.py location for compound het detection

  #103 opened 6 months ago by Naughtoncolin
  0

• Segmentationfault (core dumped) in one Chromosome

  #97 opened 6 months ago by NattyandMinnie
  1

• Bug for nonPAR chrX: heterozygous haploids in the phased output.

  #100 opened 7 months ago by dtaliun
  1

• Phase_ rare_static Error: 31mERROR: No variants to be phased!

  #63 opened a year ago by hangsuUNC
  3

• Phasing chromosome X is wrong when males are encoded as haploids in input VCF/BCF

  #99 opened 7 months ago by dtaliun
  0

• AN field in the phase_common phased data is different from the AN in unphased data

  #98 opened 8 months ago by lessdata
  0

• illegal instruction error on phase_common_static on cow array data

  #94 opened 8 months ago by lholivera
  2

• feature request: Mac OS and Linux ARM64 compatibility?

  #95 opened 8 months ago by pettyalex
  2

• Docker image - Static binaries shouldn't need host libraries

  #67 opened a year ago by pettyalex
  3

• No SER computed

  #93 opened 8 months ago by bilgetbak
  0

• Plot phasing results

  #91 opened 9 months ago by michal-yoles
  1

• No variant found

  #88 opened 10 months ago by niv280
  8

• Cannot proceed after installation

  #89 opened 10 months ago by suraya01
  0

• illegal hardware instruction

  #87 opened 10 months ago by niv280
  1

• Switch Program Output File

  #86 opened 10 months ago by AkkshayaRajesh
  0

• Interpretation of 0|0:.

  #81 opened a year ago by hara555555
  0

• Phasing of small parent-offspring sample

  #82 opened a year ago by friedav
  1

• --mcmc-noinit option doesn't work

  #84 opened a year ago by ndokmai
  0

• Phasing a Single-Sample VCF File on GRCh38

  #83 opened a year ago by lucianhu
  0

• make: *** [phase_common] Error 2

  #69 opened a year ago by PradnyaP02
  2

• Recommendations for references

  #74 opened a year ago by shahnirav1005
  0

• Undefined reference to curl

  #71 opened a year ago by PradnyaP02
  1

• AAscore software

  #73 opened a year ago by nathanLauHKGI
  1

• Working with SVs: preserve INFO/END field after phase_common

  #72 opened a year ago by dtaliun
  0

• Reproducible results

  #58 opened a year ago by zhangpicb
  5

• Read-aware Phasing

  #57 opened a year ago by hangsuUNC
  5

• SER meaurement - merge multiallelic sites first?

  #66 opened a year ago by JosephLalli
  0

• phase_common: command not found

  #64 opened a year ago by aissushan
  4

• fasta file format not supported

  #61 opened a year ago by suvi93
  3

• Rare phasing error: `Assertion V.vec_full[vt]->type == VARTYPE_SCAF failed`

  #52 opened a year ago by mvvugt
  3

• rare phasing yields PP=0.5 at all singletons

  #56 opened a year ago by giorkala
  2

• B37 chunks

  #62 opened a year ago by BEFH
  0

• "Wrong order in your genetic map file" in concatenated genetic files

  #59 opened a year ago by chunxuan-hs
  4

• Phasing with relateds as scaffold

  #60 opened a year ago by psnavais
  3

• phase_rare on small locus

  #55 opened a year ago by klmartinez
  5

• Genetic map file for T2T genome (CHM13)

  #54 opened a year ago by hangsuUNC
  2

• Segmentation fault

  #53 opened a year ago by klmartinez
  2