mskcc facets issues - Githubissues

mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

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Purity values NA and suggestions?

#204 jiwonhong95 opened 3 days ago
1
snp-pileup for mm10/GRCm38 mouse

#203 ahwanpandey opened 2 weeks ago
5
Enquiry on consistent segments amplified/deleted across most samples

#202 michelle-jahja opened 1 month ago
3
How to resolve variability in results due to different random seeds?

#201 ehhfy opened 2 months ago
4
mm39 in the preProcSample {facets}

#200 karolina16 opened 5 months ago
1
Incorrect plots with purity=NA

#199 karolina16 closed 5 months ago
0
cf.em too low?

#198 THT-sleepy opened 7 months ago
0
Can bams with marked duplicates(without removing) be used as input for snp-pileup?

#197 THT-sleepy closed 7 months ago
0
snp_pileup returning no calls.

#196 apallav21 opened 10 months ago
0
What is difference between CNCF and EM plot/algorithm?

#195 allthetime115 opened 1 year ago
0
adding line in procSnps() to ensure required field order

#194 agorelick opened 1 year ago
0
question about ploidy estimate

#193 guillaume-rs opened 1 year ago
1
cf.em is NA

#192 rabiafidan closed 1 year ago
5
run cnv_facets error for some samples, hope someone for help!!

#191 edceeyuchen closed 1 year ago
1
properly order the jointseg

#190 ShixiangWang opened 1 year ago
0
Impact of FFPE preservation

#189 mybabyfox opened 1 year ago
0
Calling CNA from Cat genome; custom

#188 makarov-ccf opened 1 year ago
3
Questions about ploidy estimate

#187 ysbioinfo opened 1 year ago
0
pythonize snp-pileup

#186 veseshan opened 1 year ago
0
the output description of the jointseg.txt

#185 litun-fkby opened 1 year ago
0
Snp-pileup failed to return data

#184 boonhaohong opened 2 years ago
8
fewer heterozygous variants

#183 jsha129 opened 2 years ago
4
Error "replacement has 0 rows", caused by dipLogR=numeric(0)

#182 ypradat opened 2 years ago
2
Generat snplocs* files

#181 Jiayi-Wang-Joey opened 2 years ago
0
Installation error

#180 Jiayi-Wang-Joey opened 2 years ago
0
MacOS installation error | clang (LLVM option parsing): Unknown command line argument '-x86-pad-for-align=false'

#179 oliverartz opened 2 years ago
2
purity is NA and how to interpret the plot

#178 stroke1989 opened 2 years ago
2
Add inst/CITATION + fix R CMD check errors

#177 HenrikBengtsson opened 2 years ago
0
WISH: Add CITATION file => citation(package = "facets") mentions paper

#176 HenrikBengtsson opened 2 years ago
0
only call individul normal bam

#175 gaom001 opened 2 years ago
0
Setting purity=1

#174 RoniHaas closed 2 years ago
6
How the kernel density of cell fraction was plotted in the paper?

#173 zh9118 opened 2 years ago
2
Is tumor purity == 0.3 invalid?

#172 davidtourigny opened 2 years ago
0
Purity NA - (with observed CN changes!)

#171 alexcoulton opened 2 years ago
0
chromosome name

#170 sotaro-kanematsu opened 3 years ago
1
FIX: Registration of the native API never took place

#169 HenrikBengtsson closed 3 years ago
0
Tidy up package and enable CI checking on GitHub Actions

#168 HenrikBengtsson closed 3 years ago
0
Yes "cnlr.median - dipLogR" is the log(total copy number) unadjusted for purity which is what you want.

#167 qindan2008 closed 3 years ago
0
how to install and use

#166 shujch opened 3 years ago
3
WGS recommendations for chromothripsis analysis

#165 ahwanpandey opened 3 years ago
0
Can not install using devtools

#164 jianxinwang opened 3 years ago
1
ERROR happened in facets when calling CNV

#163 lizhan96 closed 3 years ago
0
Reduce memory usage of facets

#162 natir opened 3 years ago
5
Facet bed: issue chromosomal position format

#161 legendre-adrien opened 3 years ago
0
dependency pctGCdata has unclear requirements

#160 jbedo closed 3 years ago
5
ndepth parameter for XX vs XY genome

#159 quentinba opened 3 years ago
0
Comparing FACETS to results from callers that calculate a relative copy number only

#158 popicka opened 4 years ago
0
ndepth in preProcSample is not suitable if can not be set as 0

#157 worker000000 opened 4 years ago
0
Can I force the ploidy to a specific value (experimentally validated) in facets?

#156 Francesc-Muyas opened 4 years ago
0
emcncf called purity NA, ploidy 2, and em flag despite passing mafR.clust cutoff

#155 sas1531 opened 4 years ago
0