cancerit/BRASS

Issues

• Brass Notation - Understanding Breakpoints

  #120 opened 5 months ago by LB1907
  2

• No data survived filtering

  #119 opened 8 months ago by ruolin
  0

• Security vulnerabilities in current container image

  #118 opened a year ago by verdurin
  0

• Iterations must be a positive integer: 0 at /opt/wtsi-cgp/bin/brass.pl line 83.

  #117 opened 2 years ago by DingTin
  2

• Poor inversion recall performance in BAM files with a high amount of variants

  #114 opened 2 years ago by Rapsssito
  3

• What kind of file does the parameter "-d" require?

  #116 opened 2 years ago by DingTin
  0

• No read groups listed

  #115 opened 2 years ago by bettinabudeus
  0

• Poor perfomance in sparse BAM files

  #113 opened 2 years ago by Rapsssito
  0

• getting POS of 0

  #110 opened 2 years ago by anoronh4
  7

• Any way to ignore PL in bam?

  #112 opened 2 years ago by anoronh4
  4

• Should be an existing file

  #111 opened 2 years ago by mdbarnesUCSD
  1

• Regions of excessive sequencing depth for hg38

  #109 opened 2 years ago by zhujack
  1

• Docker/Singularity quay.io not found

  #108 opened 3 years ago by mdbarnesUCSD
  2

• Question: Does BRASS support exomes?

  #107 opened 3 years ago by anoronh4
  1

• less *.ngscn.segments.abs_cn.bg | cut -f1 | sort -u 1 2 3 4 5 6 7 8 9 X Y

  #106 opened 3 years ago by jsmedmar
  3

• duplicate records for inversions

  #105 opened 3 years ago by sb43
  0

• Bedtools problem with get_rg_cns.R

  #104 opened 4 years ago by jsmedmar
  0

• how to optimize performance

  #103 opened 4 years ago by anoronh4
  4

• Issue with creating tmp directory

  #102 opened 4 years ago by anoronh4
  0

• unused argument (cytoband_file = cytoband_file) - caused by Rlib - gam incompatibility

  #91 opened 5 years ago by podro182
  4

• centromere telomere file

  #101 opened 4 years ago by mjko1210
  4

• Performance improvement - input step

  #100 opened 4 years ago by keiranmraine
  0

• Should give 0 exit code when detect previous analysis

  #98 opened 4 years ago by keiranmraine
  0

• brassI_prep_bam.pl - fails if RG ID is last element of header line

  #99 opened 4 years ago by keiranmraine
  0

• Document docker/singularity

  #97 opened 4 years ago by keiranmraine
  0

• Generating an input bas?

  #96 opened 4 years ago by cboursnell
  1

• Error in get_abs_bkpts_from_clipped_reads.pl

  #95 opened 5 years ago by udvzol
  8

• Sequencing protocol - misleading as indicates other than WGS/genomic

  #94 opened 5 years ago by keiranmraine
  0

• Travis CI file needs update

  #89 opened 5 years ago by rulixxx
  0

• Required params not checked

  #93 opened 5 years ago by keiranmraine
  1

• bedpe ann error

  #77 opened 6 years ago by gbnci
  10

• docker container gives errors when run from singularity

  #92 opened 5 years ago by cboursnell
  1

• Readgroup does not exist

  #90 opened 5 years ago by podro182
  4

• Sample statistics file is required

  #85 opened 5 years ago by kathryn-beal
  0

• blatSrc has moved

  #86 opened 5 years ago by keiranmraine
  0

• Fail when RG==0

  #80 opened 6 years ago by ym3
  1

• Speedup - input step

  #84 opened 6 years ago by keiranmraine
  0

• error and quit for brass run

  #75 opened 6 years ago by gbnci
  1

• Is RC the same as SR?

  #83 opened 6 years ago by ggrimes
  1

• Error: Sanger_CGP_Brass_Implement_group.0.err" unexpectedly returned exit value 1

  #81 opened 6 years ago by Dorical
  5

• conda installation issues

  #82 opened 6 years ago by alongalor
  1

• Error in get_abs_bkpts_from_clipped_reads.pl

  #66 opened 6 years ago by hfl112
  6

• Centromere/telomere file doesn't agree with example

  #69 opened 6 years ago by edawson
  2

• BRASS filter generation fails with an uninformative error when *.bas not present

  #71 opened 6 years ago by edawson
  1

• Brass produces output but returns code 255

  #73 opened 6 years ago by edawson
  9

• bedpe to vcf conversion is not correct

  #78 opened 6 years ago by zhujack
  1

• Blat path not exist

  #76 opened 6 years ago by gbnci
  0

• depth parameter

  #74 opened 6 years ago by gbnci
  1

• Implement_group error

  #67 opened 6 years ago by BastienNguyen
  6

• Clarification: Penalty for finding aberrant pairs for PON separately vs jointly

  #72 opened 6 years ago by edawson
  1