mskcc/facets

Issues

• mm39 in the preProcSample {facets}

  #200 opened 3 months ago by karolina16
  1

• Incorrect plots with purity=NA

  #199 opened 3 months ago by karolina16
  0

• Can bams with marked duplicates(without removing) be used as input for snp-pileup?

  #197 opened 6 months ago by THT-sleepy
  0

• cf.em too low?

  #198 opened 6 months ago by THT-sleepy
  0

• Snp-pileup failed to return data

  #184 opened 2 years ago by boonhaohong
  8

• snp_pileup returning no calls.

  #196 opened 9 months ago by apallav21
  0

• purity is NA and how to interpret the plot

  #178 opened 2 years ago by stroke1989
  2

• What is difference between CNCF and EM plot/algorithm?

  #195 opened a year ago by allthetime115
  0

• run cnv_facets error for some samples, hope someone for help!!

  #191 opened a year ago by edceeyuchen
  1

• question about ploidy estimate

  #193 opened a year ago by guillaume-rs
  1

• Calling CNA from Cat genome; custom

  #188 opened 2 years ago by makarov-ccf
  3

• cf.em is NA

  #192 opened a year ago by rabiafidan
  5

• Impact of FFPE preservation

  #189 opened a year ago by mybabyfox
  0

• MacOS installation error | clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'

  #179 opened 2 years ago by oliverartz
  2

• Questions about ploidy estimate

  #187 opened 2 years ago by ysbioinfo
  0

• pythonize snp-pileup

  #186 opened 2 years ago by veseshan
  0

• Purity estimate =NA despite copy numbers present

  #146 opened 5 years ago by GeorgetteTanner
  19

• the output description of the jointseg.txt

  #185 opened 2 years ago by litun-fkby
  0

• Error "replacement has 0 rows", caused by dipLogR=numeric(0)

  #182 opened 2 years ago by ypradat
  2

• fewer heterozygous variants

  #183 opened 2 years ago by jsha129
  4

• no output

  #149 opened 5 years ago by lihm1
  1

• Generat snplocs* files

  #181 opened 2 years ago by Jiayi-Wang-Joey
  0

• Installation error

  #180 opened 2 years ago by Jiayi-Wang-Joey
  0

• WISH: Add CITATION file => citation(package = "facets") mentions paper

  #176 opened 2 years ago by HenrikBengtsson
  0

• Incoherent values of LogR estimate & Total Copy number estimate

  #145 opened 5 years ago by Pacomito
  2

• only call individul normal bam

  #175 opened 2 years ago by gaom001
  0

• How the kernel density of cell fraction was plotted in the paper?

  #173 opened 3 years ago by zh9118
  2

• Setting purity=1

  #174 opened 2 years ago by RoniHaas
  6

• Is tumor purity == 0.3 invalid?

  #172 opened 3 years ago by davidtourigny
  0

• Purity NA - (with observed CN changes!)

  #171 opened 3 years ago by alexcoulton
  0

• chromosome name

  #170 opened 3 years ago by sotaro-kanematsu
  1

• snp-pileup compilation issue

  #151 opened 5 years ago by kibala93
  1

• how to install and use

  #166 opened 3 years ago by shujch
  3

• Yes "cnlr.median - dipLogR" is the log(total copy number) unadjusted for purity which is what you want.

  #167 opened 3 years ago by qindan2008
  0

• WGS recommendations for chromothripsis analysis

  #165 opened 3 years ago by ahwanpandey
  0

• Can not install using devtools

  #164 opened 3 years ago by jianxinwang
  1

• ERROR happened in facets when calling CNV

  #163 opened 3 years ago by lizhan96
  0

• dependency pctGCdata has unclear requirements

  #160 opened 4 years ago by jbedo
  5

• Facet bed: issue chromosomal position format

  #161 opened 4 years ago by legendre-adrien
  0

• ndepth parameter for XX vs XY genome

  #159 opened 4 years ago by quentinba
  0

• Some urgent questions about facets result

  #147 opened 5 years ago by ShixiangWang
  7

• Comparing FACETS to results from callers that calculate a relative copy number only

  #158 opened 4 years ago by popicka
  0

• ndepth in preProcSample is not suitable if can not be set as 0

  #157 opened 4 years ago by worker000000
  0

• Can I force the ploidy to a specific value (experimentally validated) in facets?

  #156 opened 4 years ago by Francesc-Muyas
  0

• emcncf called purity NA, ploidy 2, and em flag despite passing mafR.clust cutoff

  #155 opened 4 years ago by sas1531
  0

• segclust Missing Error

  #154 opened 4 years ago by DarioS
  0

• facets.R RAM issue

  #153 opened 4 years ago by alhafidzhamdan
  0

• Weird regions of homozygous deletion

  #152 opened 4 years ago by af8
  0

• is it a bug of emcncf

  #150 opened 5 years ago by jidixueye
  0

• Question: Should remove duplicates before using facets?

  #148 opened 5 years ago by ShixiangWang
  2