oicr-gsi/debarcer

Issues

• Missing records for different family size in merged consensus file

  #217 opened 4 years ago
  0

• Allow jobs to run on univa

  #209 opened 4 years ago
  0

• Debarcer group function does not check for empty regions

  #206 opened 4 years ago
  3

• Issues with debarcer "group" function in creating new output directory

  #205 opened 4 years ago
  0

• Keep network plot?

  #204 opened 4 years ago
  1

• Keep network plot?

  #203 opened 4 years ago
  1

• Add base quality filter

  #202 opened 4 years ago
  0

• Add parameter to specify UMI separator

  #201 opened 4 years ago
  0

• Verify read depth of the regions identified by the scanner

  #186 opened 5 years ago
  1

• Fix tick positions

  #185 opened 5 years ago
  0

• AssertionError in VCF call

  #184 opened 5 years ago
  1

• KeyError in VCF Call

  #183 opened 5 years ago
  1

• Unexpected values in yaml

  #182 opened 5 years ago
  1

• Ref base not defined

  #181 opened 5 years ago
  2

• Issue when computing tick positions

  #180 opened 5 years ago
  1

• KeyError because of missing position during plotting

  #179 opened 5 years ago
  1

• Assertion error in Collapse

  #178 opened 5 years ago
  1

• Read1 is cropped for sureselect and haloplex libraries

  #176 opened 5 years ago
  2

• Output preprocessing-filtered reads to fastqs

  #168 opened 5 years ago
  0

• Umis in paired reads

  #167 opened 5 years ago
  0

• VCF output

  #166 opened 5 years ago
  0

• Phred score is set to 0

  #162 opened 5 years ago
  1

• Update functions that read consensus files

  #155 opened 5 years ago
  2

• Output bam with consensus reads

  #151 opened 5 years ago
  1

• Reference base is not defined

  #150 opened 5 years ago
  1

• Improve allelic counts

  #148 opened 5 years ago
  1

• No need to loop through interval positions. Positions already keys in dictionary

  #147 opened 5 years ago
  0

• preprocessing

  #146 opened 5 years ago
  2

• Check that indel sequence is correct

  #145 opened 5 years ago
  1

• Exclude filtered reads when computing read depth

  #144 opened 5 years ago
  1

• plot option not available from the run module

  #143 opened 5 years ago
  1

• overlapping labels in donut plot

  #142 opened 5 years ago
  1

• generate a single VCF per consensus file

  #141 opened 5 years ago
  1

• filter secondary and supplementary alignments

  #140 opened 5 years ago
  1

• VCF output

  #139 opened 5 years ago
  0

• pysam and samtools give slightly different allele count and read depth

  #138 opened 5 years ago
  1

• unmapped reads

  #137 opened 5 years ago
  1

• Add indel sequences to VCF

  #136 opened 5 years ago
  1

• Add parameter for filter

  #135 opened 5 years ago
  1

• Extend debarcer to other library preps

  #134 opened 5 years ago
  1

• Add option to locate umi within reads

  #133 opened 5 years ago
  1

• Restrict reads to the genomic interval during umi family grouping

  #132 opened 5 years ago
  1

• Restrict positions to genomic interval

  #131 opened 5 years ago
  1

• use pysam to extract reference positions/sequence

  #130 opened 5 years ago
  0

• Ref_threshold and all_threshold

  #129 opened 5 years ago
  1

• Position is adjusted to 1-based

  #128 opened 5 years ago
  1

• Consensus table

  #127 opened 5 years ago
  0

• Mean family size lower than minimum family size

  #126 opened 5 years ago
  3

• Inconsistent used of 1-based and 0-based coordinates

  #125 opened 5 years ago
  2

• Undefined variable name

  #124 opened 5 years ago
  1