statgen/Minimac4

Issues

• Missing INFO.gz after imputation & Sample ploidy inconsistency error on chrX

  #78 opened 3 months ago by yiiruulin
  1

• Imputation of Structural Variants

  #40 opened 4 years ago by jjfarrell
  8

• record mismatch in temp files when -a option is active

  #77 opened 5 months ago by edg1983
  7

• The imputed genotypes is increased compared to the original vcf file

  #59 opened 2 years ago by liubh9
  2

• Error: failed loading target haplotypes

  #76 opened 6 months ago by TheRainInSpain
  5

• should the reference vcf file be phased

  #75 opened 6 months ago by TheRainInSpain
  1

• Inconsistent ploidy and segmentation fault when creating 1000GP chrX.PAR[1-2].msav

  #74 opened 6 months ago by youngchanpark
  1

• Error: target chromosome not found in genetic map file

  #73 opened 7 months ago by WeiYang-BAI
  3

• Specific information on HDS

  #72 opened 7 months ago by bgb-ipl
  2

• Problem with Installing

  #71 opened 7 months ago by dat4yc
  2

• Error: failed writing output

  #70 opened 8 months ago by andrei-barysenka
  5

• Reference Panel download

  #66 opened a year ago by Shrishtee-kandoi
  8

• Non-adjacent blocks from --compress-reference

  #69 opened 9 months ago by andrew-slater
  3

• Error: I/O failed while merging

  #68 opened 10 months ago by lingjoyo
  8

• Map file

  #67 opened a year ago by shiva-g
  0

• low overlapping between target panel and reference panel

  #64 opened a year ago by Zhenghongc
  4

• Combined haplotypes can't be loaded

  #65 opened a year ago by rsteinfe1
  3

• ERROR: Cannot execute binary file

  #63 opened a year ago by DavidGO464
  3

• Multithreading during M3VCF/MSAV Generation?

  #62 opened a year ago by mragsac
  3

• Different chrX ploidy in --output and --empirical-output

  #61 opened a year ago by robkar
  9

• The imputed vcf has far more genotypes than the target phased vcf and missed rsID.

  #60 opened 2 years ago by huww1998
  5

• install failed

  #41 opened 4 years ago by xiaomiyang36
  9

• Error writing output

  #55 opened 2 years ago by aokulabasile
  17

• Segmentation fault, and docs

  #57 opened 2 years ago by rlad
  34

• lack of compliance with VCF v4.3 specification

  #58 opened 2 years ago by freeseek
  1

• Auto deletion of temp files?

  #56 opened 2 years ago by eldronzhou
  1

• Segmentation fault After 'Imputation successful'

  #42 opened 2 years ago by jjfarrell
  8

• Help to upgrade test suite from version 4.0.3 to 4.1.1

  #54 opened 2 years ago by tillea
  8

• How to obtain the RS ID from Minimac4 results

  #34 opened 5 years ago by xiangboyulan
  17

• Option to Subset Samples in Reference Panel

  #28 opened 2 years ago by jonathonl
  2

• New minimac4 release v4.1.0 produces vcf.gz which can't be read by DosageConvertor

  #53 opened 2 years ago by sereeena
  14

• Imputing variants at multi-allelic sites

  #52 opened 3 years ago by thheng
  5

• How does Minimac4 handle large chunks of missing genotype when creating reference panel

  #32 opened 5 years ago by JoannaTan
  4

• Can't build from requirements.txt, zlib v1.2.11 no longer exists

  #50 opened 3 years ago by sereeena
  3

• Imputation aborted

  #46 opened 3 years ago by albaicans
  4

• Invalid VCF for two chromosomes, running Minimac through The Michigan Imputation Server

  #49 opened 3 years ago by julien-laval
  2

• bash script to show an example of eagle2 + minimac4 for phasing and imputation?

  #48 opened 3 years ago by Shicheng-Guo
  0

• Imputing population heterogeneous datasets

  #44 opened 3 years ago by albaicans
  6

• Minimac4: commercial license for pharma company usage?

  #47 opened 3 years ago by Shicheng-Guo
  1

• Imputation of 23andMe data

  #45 opened 3 years ago by Panacotaforcota
  1

• SNP ID format of input files and reference panels for imputation

  #43 opened 3 years ago by jerrywzy
  2

• What is minRatio option?

  #39 opened 4 years ago by chulghim
  1

• Calculating imputation accuracy Rsq for variants on chromosome X/23

  #38 opened 4 years ago by QinqinHuang
  0

• How does GT output in imputed vcf correspond to DS, HDS and GP? chromosome X imputation Michigan server

  #37 opened 4 years ago by tesselgalesloot
  0

• CMake Error occurred at installing minimac4

  #36 opened 4 years ago by awakumaya
  6

• Retraining on new data?

  #35 opened 4 years ago by daquang
  0

• R2 and ER2 in Minimac4 output

  #30 opened 5 years ago by ValRi78
  3

• How should missing genotypes be represented in prephased data?

  #31 opened 5 years ago by biona001
  4

• Inconsistency between vcf and m3vcf reference panels

  #29 opened 5 years ago by eyherabh
  0

• Allowing chomosome number above 22

  #27 opened 5 years ago by ChrisINRA
  3