mskcc/facets-suite

Issues

• File naming for adjusted CNLR

  #67 opened 2 months ago by tischfis
  0

• WGD status being used from hisens run in gene-level script?

  #65 opened 6 months ago by arichards2564
  0

• Potential bug in # of discordant LCN segments

  #64 opened 6 months ago by arichards2564
  0

• Singularity image - Error when output folder exists

  #63 opened 7 months ago by apallav21
  0

• Unable to library facetsPreview because Package ‘glue’ version 1.6.2 cannot be unloaded

  #62 opened 8 months ago by PollyHung
  0

• Bug in HRD-LOH calculation (copy-number-scores.R) causing loss of HRD-LOH information

  #61 opened 10 months ago by danielmuldoon
  0

• Can I run the facets-suite wrappers with unmatched normals?

  #60 opened a year ago by ssrinivasan2
  0

• Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found

  #46 opened 3 years ago by YingYa
  5

• Return numeric_val as well as cn_state

  #59 opened a year ago by pintoa1-mskcc
  0

• consider changing numeric call in copy number states

  #58 opened a year ago by tischfis
  0

• Error while running run-facets-wrapper.R

  #57 opened 2 years ago by akhileshmishra0908
  2

• Plotting incorrect metric when highlighting gene (should be valor, not cnlr)

  #56 opened 2 years ago by arichards2564
  0

• Recommended cval value for whole exome sequencing data

  #48 opened 3 years ago by hanyin88
  1

• Columns t_alt_count and t_depth required

  #55 opened 2 years ago by Rahel14350
  0

• Couldn't run one-pass mode because default "--purity-cval" value.

  #52 opened 2 years ago by zhouzhendiao
  0

• Please update docker image

  #51 opened 2 years ago by zhouzhendiao
  0

• Using Alt+Ref instead of true depth

  #50 opened 2 years ago by arichards2564
  0

• fraction_loh from copy-number-scores.R and frac_loh from check-fit.R not the same

  #47 opened 3 years ago by YingYa
  0

• Use of t_depth vs. t_alt_count + t_ref_count

  #44 opened 4 years ago by andurill
  0

• Segments with tcn.em=2 and lcn.em=NA?

  #43 opened 4 years ago by lisemangiante
  0

• Meaning of the filter column in focal copy number output

  #42 opened 4 years ago by NicolaLady
  0

• add tumor_id and normal_id for run-facets-wrapper.R

  #41 opened 4 years ago by stevekm
  0

• [bug fix] arm_level_change() gives wrong aneuploidy_score

  #39 opened 4 years ago by MajoroMask
  0

• Discarding High Amps

  #37 opened 4 years ago by arichards2564
  1

• gene_level_changes highest alteration

  #36 opened 4 years ago by BastienNguyen
  0

• Incorrect AMP filtering

  #35 opened 4 years ago by arichards2564
  0

• make run-facets-wrapper.sh run "everything" by default

  #34 opened 4 years ago by cband
  0

• rbindList vs rbind

  #33 opened 5 years ago by arichards2564
  1

• Plotting Issues

  #31 opened 5 years ago by arichards2564
  1

• fread() issue for pileup

  #25 opened 5 years ago by evanbiederstedt
  0

• Fix geneLevel.R to generate portal-friendly data_CNA.txt file

  #24 opened 5 years ago by ckandoth
  3

• Altered for WGD cases if not 4:2

  #19 opened 5 years ago by kpjonsson
  1

• CNCF algorithm output in Facets R version >= 0.5.2

  #14 opened 6 years ago by kpjonsson
  6

• FACETS QC

  #3 opened 8 years ago by alexpenson
  7

• Save header and output in outmaf

  #12 opened 8 years ago by kk988
  3

• Issues with geneLevel module

  #10 opened 9 years ago by soccin
  1

• Bug in normDepth.R

  #9 opened 9 years ago by soccin
  1

• facets gene level calls should not use file name as tumor barcode?

  #6 opened 9 years ago by lordzappo
  1