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25 Open 13 Closed
25 Open 13 Closed
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Issues list

WGD status being used from hisens run in gene-level script?
#65 opened Mar 17, 2024 by arichards2564
Potential bug in # of discordant LCN segments
#64 opened Mar 4, 2024 by arichards2564
Singularity image - Error when output folder exists
#63 opened Feb 6, 2024 by apallav21
Bug in HRD-LOH calculation (copy-number-scores.R) causing loss of HRD-LOH information
#61 opened Nov 9, 2023 by danielmuldoon
Can I run the facets-suite wrappers with unmatched normals?
#60 opened Aug 8, 2023 by ssrinivasan2
Return numeric_val as well as cn_state
#59 opened May 22, 2023 by pintoa1-mskcc
consider changing numeric call in copy number states
#58 opened May 3, 2023 by tischfis
Error while running run-facets-wrapper.R
#57 opened Feb 13, 2023 by akhileshmishra0908
2
Plotting incorrect metric when highlighting gene (should be valor, not cnlr)
#56 opened Jan 13, 2023 by arichards2564
Columns t_alt_count and t_depth required
#55 opened Oct 11, 2022 by Rahel14350
Couldn't run one-pass mode because default "--purity-cval" value.
#52 opened Jul 11, 2022 by zhouzhendiao
Please update docker image
#51 opened Jul 6, 2022 by zhouzhendiao
Using Alt+Ref instead of true depth
#50 opened Jun 6, 2022 by arichards2564
Recommended cval value for whole exome sequencing data
#48 opened Jan 4, 2022 by hanyin88
1
fraction_loh from copy-number-scores.R and frac_loh from check-fit.R not the same
#47 opened Sep 30, 2021 by YingYa
Error in ifelse(wgd, round(ploidy), 2) : object 'ploidy' not found
#46 opened Jun 3, 2021 by YingYa
5
Use of t_depth vs. t_alt_count + t_ref_count
#44 opened Sep 23, 2020 by andurill
Segments with tcn.em=2 and lcn.em=NA?
#43 opened Sep 2, 2020 by lisemangiante
Meaning of the filter column in focal copy number output
#42 opened Aug 14, 2020 by NicolaLady
add tumor_id and normal_id for run-facets-wrapper.R
#41 opened Jul 2, 2020 by stevekm
[bug fix] arm_level_change() gives wrong aneuploidy_score
#39 opened Jun 10, 2020 by MajoroMask
gene_level_changes highest alteration
#36 opened Apr 17, 2020 by BastienNguyen
Incorrect AMP filtering
#35 opened Apr 9, 2020 by arichards2564
@cband
make run-facets-wrapper.sh run "everything" by default
#34 opened Mar 24, 2020 by cband
rbindList vs rbind
#33 opened Mar 12, 2020 by arichards2564
1
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