brentp/slivar

Issues

• Finding de novo/autosomal recessive structural variants using slivar

  #132 opened 3 years ago by prasundutta87
  3

• "Unknown Impacts": splice_donor_5th_base, splice_donor_region, splice_polypyrimidine_tract

  #157 opened a year ago by wwgordon
  4

• Inquiry for vcf file

  #172 opened 6 months ago by dbswls0322
  1

• pslivar not working

  #171 opened 6 months ago by sitems
  1

• limit to only autosomes

  #170 opened 7 months ago by prasundutta87
  3

• Allelic balance on slivar output

  #169 opened 7 months ago by evgenii-s-martirosian
  0

• splice_polypyrimidine_tract

  #168 opened 7 months ago by hadasvolk
  1

• Solo analysis, phased data

  #167 opened 9 months ago by karoliinas
  2

• error message

  #166 opened 10 months ago by monaallouba
  7

• Trio exome data

  #165 opened 10 months ago by monaallouba
  0

• gnomAD v4

  #161 opened a year ago by equinne5
  8

• Wildcards in group subsetting?

  #164 opened a year ago by phillip-richmond-umoja
  3

• Hardware Requirement

  #162 opened a year ago by SplinterTao
  2

• Feature Request: Diagnostics on Duktape Errors/Warnings

  #163 opened a year ago by wwgordon
  0

• gnotate: converting BED to VCF

  #144 opened a year ago by wwgordon
  2

• Filter on CSQ numeric, pass if missing value

  #158 opened a year ago by wwgordon
  9

• Select inherited variants

  #160 opened a year ago by krukanna
  1

• filtering on INFO field

  #159 opened a year ago by equinne5
  4

• Quickstart should contain info on how to create a pedigree file and what tool is recommended for combining trio VCF into single file

  #156 opened a year ago by nurmians
  1

• slivar tsv singleton

  #155 opened a year ago by equinne5
  1

• hemizygous variants didn't get picked

  #154 opened a year ago by lindakjcao
  17

• VEP annotations other than impact?

  #146 opened 2 years ago by karynne7
  13

• Filter on INFO.AF_popmax, pass if missing value

  #153 opened a year ago by wwgordon
  3

• unknown phenotype

  #152 opened 2 years ago by axz91
  5

• missing DNMs from Strelka call

  #151 opened 2 years ago by weizhu365
  6

• function trio_denovo

  #150 opened 2 years ago by fromtotw
  1

• gnotate in v0.2.8 can fail to annotate indels >1 bp

  #149 opened 2 years ago by seboyden
  3

• DP threshold for chrX for males

  #147 opened 2 years ago by williamrowell
  0

• compound heterozygote tooling

  #143 opened 2 years ago by brentp
  3

• slivar expr : unaffected patients not selected

  #145 opened 2 years ago by gael-millot
  8

• query about PED and trio VCF

  #134 opened 2 years ago by prasundutta87
  2

• Slivar tsv functionality w/o family structure

  #127 opened 3 years ago by nbalanda23
  4

• Issues with group-expr in Mutect2 VCF

  #142 opened 2 years ago by fridells51
  0

• understanding slivar output

  #141 opened 2 years ago by prasundutta87
  5

• argument parser doesn't handle `=` in --arg=value

  #140 opened 2 years ago by tedil
  5

• Errors reported by slivar and no variants

  #139 opened 2 years ago by lindakjcao
  2

• CompHet question

  #138 opened 2 years ago by lindakjcao
  4

• group expression on customized FORMAT field is not working

  #137 opened 2 years ago by lindakjcao
  12

• make-gnotate, gnomAD filter field.

  #135 opened 3 years ago by Elliott77
  9

• missing null frequency variants

  #136 opened 2 years ago by luceamso
  2

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

  #130 opened 3 years ago by zeliasoo
  3

• CADD score filtering

  #133 opened 3 years ago by Elliott77
  2

• Column labels in annotation files

  #131 opened 3 years ago by priyambial123
  6

• trio and family expr results

  #124 opened 3 years ago by luceamso
  6

• Using SLIVAR for filtering variants

  #126 opened 3 years ago by dr-ashu-geno
  1

• Missing de novo variant

  #129 opened 3 years ago by krukanna
  2

• how can I extract \xb3 in slivar?

  #128 opened 3 years ago by luceamso
  8

• extract shared variant

  #125 opened 3 years ago by luceamso
  6

• Make gnotate from ExAC downloaded from Gnomad

  #122 opened 3 years ago by Drdreammaerd
  13

• Compound het allele segregation in multi-generational pedigree with multiple affecteds

  #123 opened 3 years ago by mvelinder
  2