facets-suite
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mskcc
Utility functions for FACETS
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/gene-level-changes.R#L45 While generally unlikely, if we're using the WGD derived from the segments from the hisens run, this could conflict with the overall call of WGD where we use the...
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/check-fit.R#L181 Is this supposed to be sum(X) as opposed to sum(length(X))?
Hi, singularity run facets-suite-dev.img run-facets-wrapper.R is exiting with exception that the output folder (-D arg) already exists. I am forced to delete the folder to re-run the program. I don't...
calculate_hrdloh function bug To reproduce the bug: find a tumor-normal sample with only one complete chromosome deletion. This deletion must be homozygous. Slack me for specific tumor-normal examples from IMPACT....
Hello, I am working with WGS data from several cell lines, using a "normal" cell line as a common normal across the cancer cell lines. Looking through the documentation for...
Hi, I am running facets-suite.v2.0.8 with "run-facets-wrapper.R --counts-file normal-VS-tumor.FACETS.pileup.gz --sample-id normal-VS-tumor --directory facets-suite --everything --genome hg38 --purity-cval 2000 --cval 1000", but some sampels were failed. n = 626733 > max_n{n...
[Oncokb CNA annotator can now accept numeric values that match GISTIC](https://docs.cbioportal.org/file-formats/#discrete-copy-number-data) Given that, can we report the numeric values in our final outputs as well? For reference: > For each...
for GAIN (many states) with WGD annotated as a -1 numeric call (TCN=5). Consider changing to 1 as it's a GAIN.
I am trying to run run-facets-wrapper.R, using this command - singularity exec facets-suite-dev.img ./run-facets-wrapper.R --counts-file XP490_V4756-XP490_S4763.snp_pileup.gz --sample-id XP490_V4756-XP490_S4763 --purity-cval 1000 --cval 500 --everything --genome hg38 --normal-depth 25 --facets-lib-path /home2/s204755/R/x86_64-pc-linux-gnu-library/3.6/ --directory...
https://github.com/mskcc/facets-suite/blob/7d54d0f67e3136bd60d94ad810a9c855df113096/R/plot-facets.R#L191