brentp/somalier

Issues

• chrX sites count

  #133 opened 3 months ago by AinaMontalban
  0

• Scaled mean depth on X - how to calculate?

  #132 opened 5 months ago by parkjooyoung99
  1

• [error] SIGSEGV: Illegal storage access. (Attempt to read from nil?) Segmentation fault (core dumped) (

  #131 opened 5 months ago by egenomics
  14

• sm1.somalier and no other output

  #130 opened 6 months ago by methionine23
  5

• Inference questions

  #129 opened 6 months ago by solcos
  0

• Relatedness color pattern issue in plot

  #126 opened 7 months ago by mirgin01
  6

• Extracted genotypes format?

  #128 opened 6 months ago by lvclark
  2

• IBS1 count

  #127 opened 7 months ago by rgve
  0

• How sex is inferred

  #124 opened 8 months ago by solcos
  1

• Why this is a male?

  #125 opened 8 months ago by solcos
  1

• sex check

  #123 opened 8 months ago by equinne5
  6

• Failing to run find-sites

  #121 opened 9 months ago by johanneskoester
  10

• SIGSEGV: Illegal storage access. (Attempt to read from nil?)

  #120 opened 9 months ago by pamelaxu213
  2

• Sex QC for one sample

  #116 opened 9 months ago by solcos
  7

• Re-use of inferred parent names in large families

  #119 opened 10 months ago by Awtum
  1

• [Question]: difference between sites.hg38.vcf.gz and sites.hg38.rna.vcf.gz

  #118 opened 10 months ago by tamuanand
  2

• Legend results in relatedness plot

  #117 opened 10 months ago by solcos
  2

• bam files without `@RG` tag

  #115 opened a year ago by mschubert
  4

• No pedigree inference in samples from same family

  #114 opened a year ago by mjlarsen
  1

• Relate Killed?

  #113 opened a year ago by kevwilhelm95
  4

• convert somalier format to VCF/PED

  #112 opened a year ago by adigenova
  2

• Sites file for metylation data

  #110 opened a year ago by GWW
  2

• SIGSEGV: Illegal storage access. (Attempt to read from nil?) during Somalier relate

  #109 opened a year ago by jlac
  10

• Clarification in relate command across genome builds

  #108 opened 2 years ago by alexiswl
  9

• sites.vcf for chm13v2 (T2T) reference

  #107 opened 2 years ago by kpalin
  5

• How're `gt_depth_mean` and `depth_mean` calculated?

  #106 opened 2 years ago by SHuang-Broad
  18

• somalier ancestry and relate freeze on writing output on BeeGFS filesystem

  #93 opened 2 years ago by edg1983
  5

• Correlating the TSV columns with HTML

  #105 opened 2 years ago by SHuang-Broad
  3

• Bioconda recipe for somalier

  #92 opened 2 years ago by tamuanand
  3

• Infer siblings with only shared father

  #104 opened 2 years ago by matthdsm
  2

• Inconsistent ancestry predictions between Somalier and Peddy

  #103 opened 2 years ago by mpj5142
  4

• Read group (RG:Z:) position in tags seems to matter and will not run without it being at the end

  #102 opened 2 years ago by JustinChu
  3

• Error with find-sites

  #96 opened 2 years ago by ashotmarg
  15

• merging somalier files for different chromosomes

  #97 opened 2 years ago by burakalver
  3

• Symlink as bam/cram input for extraction function

  #101 opened 2 years ago by JiaweiShen1116
  1

• Matching Called VCF and Uncalled CRAMs

  #100 opened 2 years ago by marcustutert
  6

• Filtering on nsites

  #99 opened 2 years ago by marcustutert
  5

• Error extracting from a VCF

  #98 opened 2 years ago by marcustutert
  1

• Increasing Number of SNPs improving inference?

  #95 opened 2 years ago by marcustutert
  2

• No output - docker

  #94 opened 2 years ago by krukanna
  4

• known mouse sites

  #91 opened 2 years ago by igordot
  5

• Sample id duplicates

  #90 opened 2 years ago by andrewpatto
  6

• Runtime with large datasets

  #89 opened 2 years ago by marcustutert
  39

• HTML report

  #83 opened 2 years ago by Danisov
  5

• Found Zero Sites

  #88 opened 2 years ago by marcustutert
  9

• n in relatedness result

  #86 opened 2 years ago by wac
  1

• Licensing

  #87 opened 2 years ago by bballew
  2

• Issue extracting variants with VCF

  #82 opened 3 years ago by holtjma
  5

• somalier ancestry : Argument list too long

  #81 opened 3 years ago by nrosewick
  3

• Comparing Results with Multiple Samples with Same Name

  #80 opened 3 years ago by brcopeland
  1