Related Issues (20)
- make run-facets-wrapper.sh run "everything" by default
- Incorrect AMP filtering
- gene_level_changes highest alteration
- Discarding High Amps HOT 1
- [bug fix] arm_level_change() gives wrong aneuploidy_score
- add tumor_id and normal_id for run-facets-wrapper.R
- Meaning of the filter column in focal copy number output
- Segments with tcn.em=2 and lcn.em=NA?
- Use of t_depth vs. t_alt_count + t_ref_count
- Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found HOT 5
- fraction_loh from copy-number-scores.R and frac_loh from check-fit.R not the same
- Recommended cval value for whole exome sequencing data HOT 1
- Using Alt+Ref instead of true depth
- Couldn't run one-pass mode because default "--purity-cval" value.
- Columns t_alt_count and t_depth required
- Plotting incorrect metric when highlighting gene (should be valor, not cnlr)
- Error while running run-facets-wrapper.R HOT 2
- consider changing numeric call in copy number states
- Return numeric_val as well as cn_state
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from facets-suite.