BoevaLab/FREEC

Issues

• Questions about the output of CNVs and the use of assess_significance

  #127 opened 2 years ago by stbio-hbh
  8

• stack smashing detected

  #154 opened 2 months ago by edeuse
  0

• Interpreting the results

  #153 opened 3 months ago by MaryGoAround
  0

• Regions missing from ratio file

  #152 opened 3 months ago by BhumikaPriyadarshini
  0

• FREEC segfaulting at "annotate copy numbers": `cannot create std::vector larger than max_size()`

  #151 opened 3 months ago by dmgie
  0

• Segmentation fault after samtools or sambamba read the BAM file

  #149 opened 5 months ago by Calhs
  2

• questions about ratio.txt

  #145 opened 6 months ago by ZYongQi
  3

• get the float copy number values

  #148 opened 5 months ago by hushuzuiniu
  2

• No normalization although it is requested

  #144 opened 5 months ago by s-juross
  2

• ERROR: there was a problem in the initial guess of the polynomial

  #123 opened 2 years ago by KamilMaliszArdigen
  8

• run with multiple control files

  #128 opened 2 years ago by lmanchon
  2

• error in running gccount

  #143 opened 8 months ago by DeMagicscience
  1

• What is the meaning of suclonal information in the _ratio.txt file

  #147 opened 5 months ago by kmavrommatis
  1

• Understanding _ratio.txt and _BAF.txt for counting informative markers

  #146 opened 5 months ago by kmavrommatis
  1

• questions about the output

  #140 opened a year ago by ZYongQi
  7

• Compilation error on Ubuntu

  #102 opened 3 years ago by SzilviaKiriakov
  6

• Some settings for WGS explaind in manual are not included in provided config file for WGS.

  #142 opened 9 months ago by monagai
  0

• missing p values in assess_significance.R

  #141 opened 10 months ago by s-juross
  0

• freec can't extract reads from bam file

  #137 opened a year ago by ZYongQi
  1

• All zero reads with segfault

  #135 opened a year ago by dgodin19
  1

• Problem making plots

  #133 opened a year ago by Gon1976
  2

• Somatic cnv issue

  #134 opened a year ago by awast
  0

• Error: to calculate BAF values

  #130 opened 2 years ago
  2

• Make graph error

  #132 opened a year ago by Gon1976
  1

• New release including makeGraph 2.0?

  #131 opened a year ago by FriederikeHanssen
  1

• failed to run segmentation on chr*

  #129 opened 2 years ago by ngualand
  0

• ERROR : Unable to open fasta file for chr22 (mm10 | WGS)

  #124 opened 2 years ago by Matheo-Lode
  4

• no colors in makeGraph2.0.R script

  #126 opened 2 years ago by kostasgalexiou
  1

• Question about the output of freec2bed.pl

  #125 opened 2 years ago by taoziyu97
  0

• LOH calls on somatic CNVs

  #114 opened 2 years ago by dmasoodfda
  44

• The problem of FREEC_ratio2Absolute.R

  #122 opened 2 years ago by xiasijian
  3

• running Control-FREEC on multiple tumor/normal paired samples

  #121 opened 2 years ago by awast
  3

• _ratio.txt output

  #117 opened 2 years ago by ashenflower
  4

• Error: your BED file with coordinates of targeted regions may contain duplicates.

  #120 opened 2 years ago by awast
  0

• How to detect LOH?

  #119 opened 2 years ago by xiasijian
  0

• input for ABSOLUTE for CCF calculation

  #118 opened 2 years ago by amootta
  5

• How to make a selection Non-human min/max ExpectedGC

  #116 opened 2 years ago by Yixiangzhang1996
  3

• Clarification of a neutral CNV

  #115 opened 2 years ago by vucinick
  2

• either 'chrFiles' or 'GCcontentProfile' must be set even a normal BAM is provided.

  #113 opened 2 years ago by sunjh22
  1

• Error: your BED file with coordinates of targeted regions may contain duplicates Check chromosome 1

  #111 opened 2 years ago by nbiqgi
  2

• Somatic CNVs

  #109 opened 2 years ago by Akazhiel
  1

• Issue running FREEC on fungal genome

  #110 opened 2 years ago by tania-k
  7

• NCBI has different annotation

  #108 opened 2 years ago by RochaLAJ
  2

• Error: unable to open file or unable to determine types for file

  #107 opened 3 years ago by stroke1989
  2

• "freec -conf <config file> -sample <mySample.bam> -control <myControl.bam> " is not used

  #105 opened 3 years ago by angeladarling
  3

• feature request: Ignore chromosomes not in caputre file instead of failing

  #106 opened 3 years ago by FriederikeHanssen
  0

• Abnormally low reads used to compute CN profile

  #103 opened 3 years ago by WillieYu
  1

• Troubles in inferring LOH

  #99 opened 3 years ago by Giuseppe1995
  4

• Help with ratio.txt file

  #100 opened 3 years ago by merckey
  2

• Segmentation fault (core dumped)

  #101 opened 3 years ago by wyqhyrz
  1