facets
facets copied to clipboard
mskcc
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Hi! My genome aligned with different builds so different snploc* files are required. I wonder how do you generate the snploc* files? Thanks, Jiayi
Hi Thanks for your work of FACETS. I am a MacOS user. And I have the following error when installation. ``` ─ installing *source* package ‘facets’ ... ** using staged...
By adding an `inst/CITATION` file with info on the FACETS paper (https://pubmed.ncbi.nlm.nih.gov/27270079/), it'll be easier to locate the reference. I'll post a PR soon.
Hello, I ran FACETS on tumor vs normal in human (breast cancer). On chromosome 2 I have values for LogR estimate and Total Copy number estimate that I don't understand:...
Hi, I just wonder if FACETS can apply for norrmal sample only without tumor sample to study individual germline copy number. Thanks in advance!
Hi, Trying to get some help from here. I am trying to make the kernel density plot which was shown in the paper. However, didn't find such a function in...
I am referencing an [issue](https://github.com/taylor-lab/facets-preview/issues/19) I opened on the FACETS preview repository, regarding a tumor purity of exactly 0.3 being flagged as invalid. Can anyone provide an explanation for this...
Hello, In the following issues, where users have derived NA purity values, the response has been that this is due to a lack of copy number changes: https://github.com/mskcc/facets/issues/66 https://github.com/mskcc/facets/issues/68 I...
I am using facets to uncover allele-specific somatic copy number alternations using clinical tumor-normal pairs. I run the cnv_facets.R script as below. cnv_facets.R --gbuild hg19 -t Tumor.bam -n Normal.bam -vcf...
