CSB5/lofreq

Issues

• How does LoFreq automatically adapt to changes in coverage?

  #148 opened 4 months ago by LiuH2020
  0

• lowfreq "not available from current channels"

  #146 opened 4 months ago by antonkratz
  1

• Lofreq viterbi

  #144 opened a year ago by rahil19
  3

• MGI T7 or T10 data

  #141 opened 5 months ago by Eduardo-Auer
  0

• Are there any suggested set of hard filters on lofreq indel file

  #145 opened 5 months ago by tanu06
  0

• Lofreq vcfplot - python version 3 support

  #143 opened a year ago by saradunaj
  0

• What are the stringent outputs and why do I have different calling results?

  #142 opened a year ago by ginnyintifa
  0

• subprocess.CalledProcessError: non-zero exit status 1

  #139 opened a year ago by balayev1
  4

• HTSLIB Variable

  #138 opened a year ago by mkadlof
  2

• IndexError: list index out of range

  #140 opened a year ago by min0609
  7

• Warning: indel calls (before filtering) were made without indel alignment-quality

  #104 opened 4 years ago by rahil19
  7

• subprocess.CalledProcessError: non-zero exit status 1

  #137 opened a year ago by balayev1
  0

• indelqual 'unknown op 3 for read' error

  #103 opened 5 years ago by mattdoug604
  9

• AF/SNV quality filters are not appliable together

  #99 opened 5 years ago by stefanches7
  2

• how to call multiple-sample variants

  #136 opened 2 years ago by ChenDepp
  4

• lofreq vcfplot issues

  #135 opened 2 years ago by Ge-Wu-pir
  2

• Permant error in the first step

  #134 opened 2 years ago by beginner984
  1

• Warning: Didn't find any variants in input

  #125 opened 3 years ago by Ram-Nagar
  2

• Problem of forget to indel alignment-quality to your bam-file

  #133 opened 2 years ago by Xiang-Leo
  4

• Lofreq call-parallel applies filters with --no-default-filter option specified

  #127 opened 3 years ago by gamabunta313
  2

• cpus count versus available cpus

  #132 opened 3 years ago by EricDeveaud
  0

• lofreq_star-2.1.5_linux-x86-64 : ./lofreq: error while loading shared libraries: libhts.so.3

  #111 opened 4 years ago by HagenC
  3

• Adding genotype information

  #117 opened 4 years ago by charlesfoster
  7

• Filter depend on number of cores?

  #131 opened 3 years ago by bernt-matthias
  0

• lofreq call-parallel will hang forever on subprocess error

  #128 opened 3 years ago by tfmorris
  0

• Using LoFreq-NQ?

  #116 opened 4 years ago by fedarko
  3

• Variants missing in parallel mode

  #123 opened 3 years ago by oleraj
  2

• lofreq p-value

  #124 opened 3 years ago by nelsonerikd
  0

• /bin/sh: line 1: 16782 Killed and CRITICAL [2021-11-30 08:43:03,767]: Following command failed with status 137

  #121 opened 3 years ago by gchevignon
  5

• No sample column

  #122 opened 3 years ago by kostasgalexiou
  0

• Quality scores

  #119 opened 4 years ago by hannahgoldswain
  1

• Problem with "lofreq call"

  #120 opened 4 years ago by MartinL1106
  0

• Force overwrite

  #118 opened 4 years ago by robinjugas
  0

• Meaning of normal_relaxed, tumor_relaxed, .._stringent (question)

  #115 opened 4 years ago by max-vdL
  0

• ERROR in temp file

  #114 opened 4 years ago by robertosirica
  1

• I have trouble to run bootstrap

  #113 opened 4 years ago by ryao-mdanderson
  3

• Missing Variant with 90% AF

  #112 opened 4 years ago by npatel-ah
  2

• Issue during the make stage

  #110 opened 4 years ago by Lakshay-sethi
  1

• Ignore non ACGT positions in reference

  #106 opened 4 years ago by andreas-wilm
  4

• merging fails during somatic variant calling (in parallel mode)

  #108 opened 4 years ago by rdmorin
  2

• Problem finding "htslib_static.mk" on make

  #105 opened 4 years ago by dnbuckley
  3

• How to enable lofreq cluster command?

  #102 opened 4 years ago by jwsohn
  1

• invalid vcf output (according to Picard)

  #101 opened 5 years ago by parlar
  1

• Running lofreq_star-2.1.5_linux-x86-64 on Linux 3.10.0-862.3.3.el7.x86_64 x86_64

  #100 opened 5 years ago by HagenC
  1

• Linux binary v2.1.5 should have statically linked dependencies

  #98 opened 5 years ago by brendanofallon
  4

• Confirm that --max-depth is per-base coverage

  #97 opened 5 years ago by rspreafico-vir
  2

• GLIBC problem during installation

  #96 opened 5 years ago by sleyn
  1

• No output?

  #93 opened 5 years ago by vymao
  3

• Handling of soft-clipped bases

  #94 opened 5 years ago by rspreafico-vir
  2

• Error when specifying --min-cov parameter

  #92 opened 5 years ago by cjuigne
  2