No segments/genes with total copy number 0 in *genes.tsv output files of PureCN

[rgraus]

Describe the issue
I have WES data from cancer cell lines established from tumor samples in our lab. I dont have corresponding, matched normal healthy samples, but we have sequenced a number of non-malignant, cancer associated fibroblasts, that I use as process-matched normal samples. I realized that in the genes.tsv files there is not a single gene with a value of 0 in the C column (the minimum value is 0.42; all other values are > 0.5).
Also, in the "type" column of genes.tsv files, there is just one deletion, in all samples.

table(tib_v_tumorSampleId_c_genes$type, useNA = "ifany")
# AMPLIFICATION      DELETION          <NA> 
#         6389             1        979333 

Related to that: I know from some cell lines based on aCGH data that they have a homozygous deletion in a gene, but when I look for that gene in genes.tsv file of the respective samples, this gene is missing in the genes.tsv file.

To Reproduce
This is the PureCN.R command:

Rscript "$purecn/PureCN.R" \
    --out "$outdir" \
    --tumor "$cov" \
    --sampleid "$s" \
    --vcf "$VCF" \
    --normaldb "$normaldb" \
    --mapping-bias-file "$mapping_bias" \
    --intervals "$intervals" \
    --snp-blacklist "$SNP_BLACKLIST" \
    --genome hg38 \
    --min-base-quality 20 \
  --min-purity 0.9 \
  --max-purity 0.99 \
  --max-copy-number 8 \
  --cosmic-cnt-info-field "CNT" \
  --cosmic-vcf-file "$COSMIC_VCF" \
    --min-cosmic-cnt 6 \
    --fun-segmentation PSCBS \
    --model-homozygous \
    --post-optimize \
    --max-segments 500 \
    --out-vcf \
  --cores 4 \
  --force \
  --seed 123

Expected behavior
I would have expected more homozygous deletions, based on previous aCGH from replicates.

Log file

cat ./results/VUC133_946_T/VUC040_R1_TI_C/VUC040_R1_TI_C.log
INFO [2026-03-01 11:20:55] ------------------------------------------------------------
INFO [2026-03-01 11:20:55] PureCN 2.14.1
INFO [2026-03-01 11:20:55] ------------------------------------------------------------
INFO [2026-03-01 11:20:55] Arguments: -tumor.coverage.file /scratch/rgraus29/projects/031_wesB1_b2_afterSarek/analysis/rgraus29/issue7_sarekDownstreamMutectNew/022_cl_pureCn_VucVufsCemm/coverage_files/cellLines/VUC040_R1_TI_C.recal_coverage_loess.txt.gz -log.ratio  -seg.file  -vcf.file ../021_sarekMutectCemmVucVufsTumOnly/results/sarek_VucVufCemmTumOnlyPureCnSet/variant_calling/mutect2/VUC040_R1_TI_C/VUC040_R1_TI_C.mutect2.filtered.vcf.gz -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf reference_files/mapping_bias_twist_hg38.rds -args.filterIntervals 100,0.05 -args.segmentation 0.005,NULL, -sampleid VUC040_R1_TI_C -min.ploidy 1.4 -max.ploidy 6 -test.purity 0.9,0.91,0.92,0.93,0.94,0.95,0.96,0.97,0.98,0.99 -max.non.clonal 0.2 -max.homozygous.loss 0.05,1e+07 -log.ratio.calibration 0.1 -model.homozygous TRUE -error 0.001 -interval.file ../014_cl_pureCn_muParamPaddingVarNotInDb/reference_files/twist_baits_hg38_intervals_p100_noOffTarget.txt -min.logr.sdev 0.15 -max.segments 500 -plot.cnv TRUE -vcf.field.prefix PureCN. -cosmic.vcf.file  -DB.info.flag DB -POPAF.info.field POP_AF -Cosmic.CNT.info.field Cosmic.CNT -model beta -post.optimize TRUE -log.file results/VUC133_946_T/VUC040_R1_TI_C/VUC040_R1_TI_C.log -normal.coverage.file <data> -normalDB <data> -args.filterVcf <data> -fun.segmentation <data> -test.num.copy <data> -speedup.heuristics <data> -BPPARAM <data>
INFO [2026-03-01 11:20:55] Using BiocParallel for parallel optimization.
INFO [2026-03-01 11:20:55] Loading coverage files...
INFO [2026-03-01 11:21:00] Mean target coverages: 103X (tumor) 100X (normal).
INFO [2026-03-01 11:21:01] Mean coverages: chrX: 89.59, chrY: 3.31, chr1-22: 101.94.
INFO [2026-03-01 11:21:01] Mean coverages: chrX: 120.71, chrY: 3.17, chr1-22: 101.45.
INFO [2026-03-01 11:21:13] Removing 13451 intervals with missing log.ratio.
INFO [2026-03-01 11:21:14] Removing 3 low/high GC targets.
INFO [2026-03-01 11:21:14] Removing 1745 intervals excluded in normalDB.
INFO [2026-03-01 11:21:14] Removing 5 intervals with low total coverage in normal (< 150.00 reads).
INFO [2026-03-01 11:21:14] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2026-03-01 11:21:14] Removing 80 low count (< 100 total reads) intervals.
INFO [2026-03-01 11:21:14] Removing 9 non-diploid allosome intervals.
INFO [2026-03-01 11:21:14] Using 232317 intervals (232317 on-target, 0 off-target).
INFO [2026-03-01 11:21:15] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2026-03-01 11:21:16] AT/GC dropout: 1.01 (tumor), 1.06 (normal), 0.97 (coverage log-ratio). 
WARN [2026-03-01 11:21:16] High GC-bias in normalized tumor vs normal log2 ratio.
INFO [2026-03-01 11:21:16] Loading VCF...
INFO [2026-03-01 11:21:19] Found 75993 variants in VCF file.
INFO [2026-03-01 11:21:19] Removing 2564 triallelic sites.
INFO [2026-03-01 11:21:19] Maximum of POPAF INFO is > 1, assuming -log10 scaled values
WARN [2026-03-01 11:21:19] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2026-03-01 11:21:20] 36609 (49.9%) variants annotated as likely germline (DB INFO flag).
WARN [2026-03-01 11:21:21] Found 1 variants with missing allelic fraction starting with chr20:2652734_G/A. Removing them.
INFO [2026-03-01 11:21:21] VUC040_VUC040_R1_TI_C is tumor in VCF file.
INFO [2026-03-01 11:21:23] 545 homozygous and 76 heterozygous variants on chrX.
INFO [2026-03-01 11:21:23] Sex from VCF: M (Fisher's p-value: < 0.0001, odds-ratio: 4.77).
WARN [2026-03-01 11:21:23] Sex mismatch of coverage and VCF. Could be because of noisy data, contamination, loss of chrY or a mis-alignment of coverage and VCF.
INFO [2026-03-01 11:21:23] Detected MuTect2 VCF.
INFO [2026-03-01 11:21:23] Removing 28683 Mutect2 calls due to blacklisted failure reasons.
INFO [2026-03-01 11:21:24] Removing 48 low quality variants with non-offset BQ < 20.
INFO [2026-03-01 11:21:24] Base quality scores range from 19 to 42 (offset by 1)
INFO [2026-03-01 11:21:24] Minimum number of supporting reads ranges from 2 to 27, depending on coverage and BQS.
INFO [2026-03-01 11:21:28] Initial testing for significant sample cross-contamination: unlikely
INFO [2026-03-01 11:21:28] Removing 7571 variants with AF < 0.030 or AF >= Inf or insufficient supporting reads or depth < 15.
INFO [2026-03-01 11:21:36] Removing 2160 blacklisted variants.
INFO [2026-03-01 11:21:36] Total size of targeted genomic region: 70.11Mb (86.74Mb with 50bp padding).
INFO [2026-03-01 11:21:37] 14.1% of targets contain variants.
INFO [2026-03-01 11:21:37] Removing 675 variants outside intervals.
INFO [2026-03-01 11:21:37] Setting somatic prior probabilities for likely germline hits to 0.000500 or to 0.500000 otherwise.
INFO [2026-03-01 11:21:37] Loading mapping bias file mapping_bias_twist_hg38.rds...
INFO [2026-03-01 11:21:38] Found 709342 variants in mapping bias file.
INFO [2026-03-01 11:21:42] Imputing mapping bias for 732 variants...
INFO [2026-03-01 11:21:55] Excluding 10267 novel or poor quality variants from segmentation.
INFO [2026-03-01 11:21:55] Sample sex: F
INFO [2026-03-01 11:21:55] Segmenting data...
INFO [2026-03-01 11:21:55] Interval weights found, will use weighted PSCBS.
INFO [2026-03-01 11:21:55] MAPD of 23990 allelic fractions: 0.00 (0.03 adjusted).
INFO [2026-03-01 11:21:56] Setting undo.SD parameter to 0.750000.
INFO [2026-03-01 11:22:51] Found 713 segments, exceeding max.segments threshold of 500.
INFO [2026-03-01 11:22:51] Setting undo.SD parameter to 1.125000.
INFO [2026-03-01 11:23:37] Setting prune.hclust.h parameter to 0.200000.
INFO [2026-03-01 11:23:39] Found 419 segments with median size of 0.56Mb.
INFO [2026-03-01 11:23:39] Using 34291 variants.
INFO [2026-03-01 11:23:40] Mean standard deviation of log-ratios: 0.23 (MAPD: 0.18)
INFO [2026-03-01 11:23:40] 2D-grid search of purity and ploidy...
INFO [2026-03-01 11:23:49] Local optima: 0.9/4.4, 0.97/5.6, 0.9/2.2, 0.9/3.4, 0.9/1.4
INFO [2026-03-01 11:23:50] Testing local optimum 1/5 at purity 0.90 and total ploidy 4.40...
INFO [2026-03-01 11:23:50] Testing local optimum 2/5 at purity 0.97 and total ploidy 5.60...
INFO [2026-03-01 11:23:50] Testing local optimum 3/5 at purity 0.90 and total ploidy 2.20...
INFO [2026-03-01 11:23:50] Testing local optimum 4/5 at purity 0.90 and total ploidy 3.40...
INFO [2026-03-01 11:23:50] Testing local optimum 5/5 at purity 0.90 and total ploidy 1.40...
INFO [2026-03-01 11:23:55] Recalibrating log-ratios...
INFO [2026-03-01 11:23:55] Testing local optimum 2/5 at purity 0.97 and total ploidy 5.60...
INFO [2026-03-01 11:23:55] Recalibrating log-ratios...
INFO [2026-03-01 11:23:55] Testing local optimum 5/5 at purity 0.90 and total ploidy 1.40...
INFO [2026-03-01 11:24:01] Recalibrating log-ratios...
INFO [2026-03-01 11:24:01] Testing local optimum 5/5 at purity 0.90 and total ploidy 1.40...
INFO [2026-03-01 11:24:08] Recalibrating log-ratios...
INFO [2026-03-01 11:24:08] Testing local optimum 5/5 at purity 0.90 and total ploidy 1.40...
INFO [2026-03-01 11:24:14] Recalibrating log-ratios...
INFO [2026-03-01 11:24:14] Testing local optimum 4/5 at purity 0.90 and total ploidy 3.40...
INFO [2026-03-01 11:24:17] Recalibrating log-ratios...
INFO [2026-03-01 11:24:17] Testing local optimum 2/5 at purity 0.97 and total ploidy 5.60...
INFO [2026-03-01 11:24:39] Recalibrating log-ratios...
INFO [2026-03-01 11:24:39] Testing local optimum 2/5 at purity 0.97 and total ploidy 5.60...
INFO [2026-03-01 11:24:40] Recalibrating log-ratios...
INFO [2026-03-01 11:24:40] Testing local optimum 4/5 at purity 0.90 and total ploidy 3.40...
INFO [2026-03-01 11:24:46] Recalibrating log-ratios...
INFO [2026-03-01 11:24:46] Testing local optimum 4/5 at purity 0.90 and total ploidy 3.40...
INFO [2026-03-01 11:25:03] Skipping 2 solutions exceeding max.non.clonal (0.20): 0.99/1.1, 0.9/1.33 (purity/tumor ploidy)
INFO [2026-03-01 11:25:03] Fitting variants with beta model for local optimum 1/5...
INFO [2026-03-01 11:25:04] Fitting variants with beta model for local optimum 2/5...
INFO [2026-03-01 11:25:04] Fitting variants with beta model for local optimum 3/5...
INFO [2026-03-01 11:25:05] Fitting variants for purity 0.95, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:25:05] Fitting variants for purity 0.97, tumor ploidy 4.93 and contamination 0.01.
INFO [2026-03-01 11:25:06] Fitting variants for purity 0.90, tumor ploidy 2.43 and contamination 0.01.
INFO [2026-03-01 11:27:35] Fitting variants for purity 0.91, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:27:38] Rare karyotype solution. Skipping post-optimization.
INFO [2026-03-01 11:27:38] Optimized purity: 0.97
INFO [2026-03-01 11:27:39] Fitting variants for purity 0.91, tumor ploidy 2.43 and contamination 0.01.
INFO [2026-03-01 11:30:06] Fitting variants for purity 0.92, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:30:09] Fitting variants for purity 0.92, tumor ploidy 2.43 and contamination 0.01.
INFO [2026-03-01 11:32:38] Fitting variants for purity 0.93, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:32:41] Fitting variants for purity 0.93, tumor ploidy 2.43 and contamination 0.01.
INFO [2026-03-01 11:35:06] Fitting variants for purity 0.94, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:35:10] Fitting variants for purity 0.94, tumor ploidy 2.43 and contamination 0.01.
INFO [2026-03-01 11:37:38] Fitting variants for purity 0.96, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:37:42] Optimized purity: 0.94
INFO [2026-03-01 11:40:09] Fitting variants for purity 0.97, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:42:37] Fitting variants for purity 0.98, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:45:07] Fitting variants for purity 0.99, tumor ploidy 3.69 and contamination 0.01.
INFO [2026-03-01 11:47:38] Optimized purity: 0.97
INFO [2026-03-01 11:47:38] Done.
INFO [2026-03-01 11:47:38] ------------------------------------------------------------
INFO [2026-03-01 11:47:43] Generating output files...
INFO [2026-03-01 11:47:59] Tumor/normal noise ratio: 13.362
WARN [2026-03-01 11:47:59] Extensive noise in tumor compared to normals.
INFO [2026-03-01 11:47:59] Using BiocParallel for parallel optimization.

B-allele frequency plot
This is the screenshot from the plots on page 2 of the sample.pdf file of the most likely solution:

Session Info

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] qs2_0.1.4                   SummarizedExperiment_1.38.1
 [3] Biobase_2.68.0              GenomicRanges_1.60.0       
 [5] GenomeInfoDb_1.44.3         IRanges_2.42.0             
 [7] S4Vectors_0.48.0            BiocGenerics_0.54.1        
 [9] generics_0.1.3              MatrixGenerics_1.20.0      
[11] matrixStats_1.5.0           here_1.0.1                 
[13] rio_1.2.3                   data.table_1.17.0          
[15] magrittr_2.0.3              lubridate_1.9.4            
[17] forcats_1.0.0               stringr_1.5.1              
[19] dplyr_1.1.4                 purrr_1.0.4                
[21] readr_2.1.5                 tidyr_1.3.1                
[23] tibble_3.2.1                ggplot2_3.5.1              
[25] tidyverse_2.0.0            

loaded via a namespace (and not attached):
 [1] gtable_0.3.6            xfun_0.51               lattice_0.22-7         
 [4] tzdb_0.4.0              vctrs_0.6.5             tools_4.5.1            
 [7] parallel_4.5.1          pkgconfig_2.0.3         R.oo_1.27.0            
[10] Matrix_1.7-4            RcppParallel_5.1.10     lifecycle_1.0.4        
[13] GenomeInfoDbData_1.2.14 compiler_4.5.1          munsell_0.5.1          
[16] DESeq2_1.48.2           codetools_0.2-20        pillar_1.10.1          
[19] crayon_1.5.3            R.utils_2.13.0          BiocParallel_1.42.2    
[22] DelayedArray_0.34.1     abind_1.4-8             locfit_1.5-9.11        
[25] zip_2.3.2               tidyselect_1.2.1        stringi_1.8.4          
[28] rprojroot_2.0.4         grid_4.5.1              colorspace_2.1-1       
[31] cli_3.6.4               SparseArray_1.8.1       S4Arrays_1.8.1         
[34] utf8_1.2.4              withr_3.0.2             scales_1.3.0           
[37] UCSC.utils_1.4.0        bit64_4.6.0-1           timechange_0.3.0       
[40] XVector_0.48.0          httr_1.4.7              bit_4.5.0.1            
[43] R.methodsS3_1.8.2       hms_1.1.3               stringfish_0.16.0      
[46] openxlsx_4.2.8          evaluate_1.0.3          knitr_1.49             
[49] rlang_1.1.5             Rcpp_1.0.14             glue_1.8.0             
[52] pkgload_1.4.1           vroom_1.6.5             jsonlite_1.9.0         
[55] R6_2.6.1

[lima1]

Apologies for the long delay and thanks for providing everything here. The ploidy is likely wrong. That can happen with cell lines where the signal should be strong, but noise, sub-clonality etc. can be elevated. Here chromosome 1 is a poor fit that likely forced a high ploidy solution. Is there a lower ploidy solution listed in the PDF?