Error in if (opt$out_vcf)

[HuZhuocheng]

Dear Author,
Hello and thank you very much for the software you have developed. When I ran ten test samples, I found that five of them produced an error message that I haven't seen in any other issues:
Warning message:
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
INFO [2025-08-17 22:25:38] Generating output files...
Warning messages:
1: In par(par.mar) : argument 1 does not name a graphical parameter
2: In par(par.mar) : argument 1 does not name a graphical parameter
3: In par(par.mar) : argument 1 does not name a graphical parameter
4: In par(par.mar) : argument 1 does not name a graphical parameter
5: In par(par.mar) : argument 1 does not name a graphical parameter
6: In par(par.mar) : argument 1 does not name a graphical parameter
7: In par(par.mar) : argument 1 does not name a graphical parameter
Error in if (opt$outvcf) { : missing value where TRUE/FALSE needed
Execution halted
My samples are from hybrid target panel sequencing without matched normal samples; there are only nine unpaired normal samples. I first ran CNVkit, and since I noticed a lot of noise in the antitarget regions, I used only the target regions and filtered the bed regions. Then I ran pureCN using the results from CNVkit and mutect2 in tumor-only mode. For mutect2, I followed your suggestion and added --interval-padding 100. My Mutect2 command is as follows:
bash
$gatk --java-options "-Xmx20G" Mutect2
-R $refGeno
-I 03MarkBQSR/BQSR$id.bam
-L $bed
--af-of-alleles-not-in-resource 0.0000025
--germline-resource $germline
--panel-of-normals $PON
--f1r2-tar-gz 04Mutect/f1r2.tar.gz
--interval-padding 100
-O 04Mutect/$id.vcf.gz
-bamout 04Mutect/$id.bam
My pureCN run script is as follows:
bash
Rscript /picb/miniconda/envs/NGS/lib/R/library/PureCN/extdata/PureCN.R
--out "$result/$id"
--sampleid "$id"
--tumor "$cnv/cancerCnr/${id}.cnr"
--seg-file "$cnv/export/${id}.seg"
--mapping-bias-file "/PureCN/reference/GenomicsDB/mappingbiashg38.rds"
--vcf "/picb/qilab/stu.04.huzhuocheng/NGS/RuijinDLBCL/$id/05mutectControl/$id.vcf"
--out-vcf "/mnt/storage1/project/NGS/callCNV/purecn/result/annoVcf/$id.anno.vcf"
--sex "$sex"
--genome hg38
--popaf-info-field POPAF
--fun-segmentation Hclust
--min-base-quality 20
--min-fraction-offtarget 1
--force --post-optimize --seed 123
Could you please advise what might be causing this issue and how I can improve it?

Here is an example of the overall run output:
Warning message:
package ‘futile.logger’ was built under R version 4.3.3
[1] "/mnt/storage1/stu.04.huzhuocheng/project/NGS/callCNV/purecn/result/0817_10test_hclust_stats"
INFO [2025-08-17 22:22:25] Loading PureCN 2.8.1...
There were 13 warnings (use warnings() to see them)
INFO [2025-08-17 22:22:25] ------------------------------------------------------------
INFO [2025-08-17 22:22:25] PureCN 2.8.1
INFO [2025-08-17 22:22:25] ------------------------------------------------------------
INFO [2025-08-17 22:22:25] Arguments: -normal.coverage.file -tumor.coverage.file /mnt/storage1/stu.04.huzhuocheng/project/NGS/callCNV/cnvkit/result/cancerCnr/RA202406190149.cnr -log.ratio -seg.file /mnt/storage1/stu.04.huzhuocheng/project/NGS/callCNV/cnvkit/result/export/RA202406190149.seg -vcf.file /picb/qilab/stu.04.huzhuocheng/NGS/RuijinDLBCL/RA202406190149/05mutectControl/RA202406190149.vcf -normalDB -genome hg38 -sex F -args.setPriorVcf 6 -args.setMappingBiasVcf /picb/qilab/stu.04.huzhuocheng/NGS/PureCN/reference/GenomicsDB/mapping_bias_hg38.rds -args.filterIntervals 100,1 -args.segmentation 0.005,NULL, -sampleid RA202406190149 -min.ploidy 1.4 -max.ploidy 6 -max.non.clonal 0.2 -max.homozygous.loss 0.05,1e+07 -log.ratio.calibration 0.1 -model.homozygous FALSE -error 0.001 -interval.file -min.logr.sdev 0.15 -max.segments 300 -plot.cnv TRUE -vcf.field.prefix PureCN. -cosmic.vcf.file -DB.info.flag DB -POPAF.info.field POPAF -Cosmic.CNT.info.field Cosmic.CNT -model beta -post.optimize TRUE -BPPARAM -log.file /mnt/storage1/stu.04.huzhuocheng/project/NGS/callCNV/purecn/result/0817_10test_hclust_stats/RA202406190149.log -args.filterVcf -fun.segmentation -test.num.copy -test.purity -speedup.heuristics
INFO [2025-08-17 22:22:25] Loading coverage files...
INFO [2025-08-17 22:22:26] Found log2-ratio in tumor coverage data.
WARN [2025-08-17 22:22:26] log2-ratio contains outliers < -8, ignoring them...
INFO [2025-08-17 22:22:26] Removing 1 intervals with missing log.ratio.
INFO [2025-08-17 22:22:26] Using 4686 intervals (4686 on-target, 0 off-target).
INFO [2025-08-17 22:22:26] No off-target intervals. If this is hybrid-capture data, consider adding them.
INFO [2025-08-17 22:22:26] Loading VCF...
INFO [2025-08-17 22:22:27] Found 19744 variants in VCF file.
INFO [2025-08-17 22:22:27] Removing 833 triallelic sites.
INFO [2025-08-17 22:22:27] Maximum of POPAP INFO is > 1, assuming -log10 scaled values
WARN [2025-08-17 22:22:27] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead.
INFO [2025-08-17 22:22:27] 2239 (11.8%) variants annotated as likely germline (DB INFO flag).
INFO [2025-08-17 22:22:27] RA202406190149 is tumor in VCF file.
INFO [2025-08-17 22:22:28] 8 homozygous and 14 heterozygous variants on chrX.
INFO [2025-08-17 22:22:28] Sex from VCF: F (Fisher's p-value: 0.825, odds-ratio: 1.09).
INFO [2025-08-17 22:22:28] Detected MuTect2 VCF.
INFO [2025-08-17 22:22:28] Removing 17645 Mutect2 calls due to blacklisted failure reasons.
INFO [2025-08-17 22:22:28] Removing 10 low quality variants with non-offset BQ < 20.
INFO [2025-08-17 22:22:28] Base quality scores range from 19 to 39 (offset by 1)
INFO [2025-08-17 22:22:28] Minimum number of supporting reads ranges from 2 to 41, depending on coverage and BQS.
INFO [2025-08-17 22:22:29] Initial testing for significant sample cross-contamination: unlikely
INFO [2025-08-17 22:22:29] Removing 637 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15.
INFO [2025-08-17 22:22:29] Total size of targeted genomic region: 1.13Mb (1.38Mb with 50bp padding).
INFO [2025-08-17 22:22:29] 8.4% of targets contain variants.
INFO [2025-08-17 22:22:29] Removing 232 variants outside intervals.
INFO [2025-08-17 22:22:29] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2025-08-17 22:22:29] Loading mapping bias file mapping_bias_hg38.rds...
INFO [2025-08-17 22:22:33] Found 1362298 variants in mapping bias file.
INFO [2025-08-17 22:22:33] Imputing mapping bias for 38 variants...
INFO [2025-08-17 22:22:37] Excluding 59 novel or poor quality variants from segmentation.
INFO [2025-08-17 22:22:37] Sample sex: F
INFO [2025-08-17 22:22:37] Segmenting data...
INFO [2025-08-17 22:22:37] Loaded provided segmentation file RA202406190149.seg (format DNAcopy).
INFO [2025-08-17 22:22:37] Re-centering provided segment means (offset -0.0388).
INFO [2025-08-17 22:22:37] Setting prune.hclust.h parameter to 0.100000.
INFO [2025-08-17 22:22:37] Found 48 segments with median size of 37.02Mb.
INFO [2025-08-17 22:22:37] Removing 1 variants outside segments.
INFO [2025-08-17 22:22:37] Using 386 variants.
INFO [2025-08-17 22:22:37] Mean standard deviation of log-ratios: 0.29 (MAPD: 0.18)
INFO [2025-08-17 22:22:37] 2D-grid search of purity and ploidy...
INFO [2025-08-17 22:22:42] Local optima: 0.19/2.8, 0.29/2.4, 0.23/2.2, 0.31/2, 0.55/2.6, 0.38/2.8,
0.42/4, 0.58/3.2, 0.55/4.2, 0.68/5.4, 0.52/3.6, 0.82/6, 0.88/5.6,
0.75/2.8, 0.92/3, 0.45/1.6, 0.62/2.1, 0.78/2, 0.62/1.4
INFO [2025-08-17 22:22:42] Testing local optimum 1/19 at purity 0.19 and total ploidy 2.80...
INFO [2025-08-17 22:22:42] Testing local optimum 2/19 at purity 0.29 and total ploidy 2.40...
INFO [2025-08-17 22:22:43] Testing local optimum 3/19 at purity 0.23 and total ploidy 2.20...
INFO [2025-08-17 22:22:44] Testing local optimum 4/19 at purity 0.31 and total ploidy 2.00...
INFO [2025-08-17 22:22:44] Testing local optimum 5/19 at purity 0.55 and total ploidy 2.60...
INFO [2025-08-17 22:22:45] Testing local optimum 6/19 at purity 0.38 and total ploidy 2.80...
INFO [2025-08-17 22:22:45] Testing local optimum 7/19 at purity 0.42 and total ploidy 4.00...
INFO [2025-08-17 22:22:46] Recalibrating log-ratios...
INFO [2025-08-17 22:22:46] Testing local optimum 7/19 at purity 0.42 and total ploidy 4.00...
INFO [2025-08-17 22:22:46] Recalibrating log-ratios...
INFO [2025-08-17 22:22:46] Testing local optimum 7/19 at purity 0.42 and total ploidy 4.00...
INFO [2025-08-17 22:22:47] Recalibrating log-ratios...
INFO [2025-08-17 22:22:47] Testing local optimum 7/19 at purity 0.42 and total ploidy 4.00...
INFO [2025-08-17 22:22:48] Testing local optimum 8/19 at purity 0.58 and total ploidy 3.20...
INFO [2025-08-17 22:22:49] Recalibrating log-ratios...
INFO [2025-08-17 22:22:49] Testing local optimum 8/19 at purity 0.58 and total ploidy 3.20...
INFO [2025-08-17 22:22:50] Recalibrating log-ratios...
INFO [2025-08-17 22:22:50] Testing local optimum 8/19 at purity 0.58 and total ploidy 3.20...
INFO [2025-08-17 22:22:51] Recalibrating log-ratios...
INFO [2025-08-17 22:22:51] Testing local optimum 8/19 at purity 0.58 and total ploidy 3.20...
INFO [2025-08-17 22:22:51] Testing local optimum 9/19 at purity 0.55 and total ploidy 4.20...
INFO [2025-08-17 22:22:52] Recalibrating log-ratios...
INFO [2025-08-17 22:22:52] Testing local optimum 9/19 at purity 0.55 and total ploidy 4.20...
INFO [2025-08-17 22:22:53] Recalibrating log-ratios...
INFO [2025-08-17 22:22:53] Testing local optimum 9/19 at purity 0.55 and total ploidy 4.20...
INFO [2025-08-17 22:22:54] Recalibrating log-ratios...
INFO [2025-08-17 22:22:54] Testing local optimum 9/19 at purity 0.55 and total ploidy 4.20...
INFO [2025-08-17 22:22:55] Testing local optimum 10/19 at purity 0.68 and total ploidy 5.40...
INFO [2025-08-17 22:22:55] Recalibrating log-ratios...
INFO [2025-08-17 22:22:55] Testing local optimum 10/19 at purity 0.68 and total ploidy 5.40...
INFO [2025-08-17 22:22:55] Recalibrating log-ratios...
INFO [2025-08-17 22:22:55] Testing local optimum 10/19 at purity 0.68 and total ploidy 5.40...
INFO [2025-08-17 22:22:56] Recalibrating log-ratios...
INFO [2025-08-17 22:22:56] Testing local optimum 10/19 at purity 0.68 and total ploidy 5.40...
INFO [2025-08-17 22:22:56] Testing local optimum 11/19 at purity 0.52 and total ploidy 3.60...
INFO [2025-08-17 22:22:56] Recalibrating log-ratios...
INFO [2025-08-17 22:22:56] Testing local optimum 11/19 at purity 0.52 and total ploidy 3.60...
INFO [2025-08-17 22:22:57] Recalibrating log-ratios...
INFO [2025-08-17 22:22:57] Testing local optimum 11/19 at purity 0.52 and total ploidy 3.60...
INFO [2025-08-17 22:22:57] Recalibrating log-ratios...
INFO [2025-08-17 22:22:57] Testing local optimum 11/19 at purity 0.52 and total ploidy 3.60...
INFO [2025-08-17 22:22:58] Testing local optimum 12/19 at purity 0.82 and total ploidy 6.00...
INFO [2025-08-17 22:22:58] Recalibrating log-ratios...
INFO [2025-08-17 22:22:58] Testing local optimum 12/19 at purity 0.82 and total ploidy 6.00...
INFO [2025-08-17 22:22:58] Recalibrating log-ratios...
INFO [2025-08-17 22:22:58] Testing local optimum 12/19 at purity 0.82 and total ploidy 6.00...
INFO [2025-08-17 22:22:59] Recalibrating log-ratios...
INFO [2025-08-17 22:22:59] Testing local optimum 12/19 at purity 0.82 and total ploidy 6.00...
INFO [2025-08-17 22:22:59] Testing local optimum 13/19 at purity 0.88 and total ploidy 5.60...
INFO [2025-08-17 22:23:00] Recalibrating log-ratios...
INFO [2025-08-17 22:23:00] Testing local optimum 13/19 at purity 0.88 and total ploidy 5.60...
INFO [2025-08-17 22:23:01] Recalibrating log-ratios...
INFO [2025-08-17 22:23:01] Testing local optimum 13/19 at purity 0.88 and total ploidy 5.60...
INFO [2025-08-17 22:23:01] Recalibrating log-ratios...
INFO [2025-08-17 22:23:01] Testing local optimum 13/19 at purity 0.88 and total ploidy 5.60...
INFO [2025-08-17 22:23:02] Testing local optimum 14/19 at purity 0.75 and total ploidy 2.80...
INFO [2025-08-17 22:23:03] Testing local optimum 15/19 at purity 0.92 and total ploidy 3.00...
INFO [2025-08-17 22:23:03] Testing local optimum 16/19 at purity 0.45 and total ploidy 1.60...
INFO [2025-08-17 22:23:04] Recalibrating log-ratios...
INFO [2025-08-17 22:23:04] Testing local optimum 16/19 at purity 0.45 and total ploidy 1.60...
INFO [2025-08-17 22:23:04] Recalibrating log-ratios...
INFO [2025-08-17 22:23:04] Testing local optimum 16/19 at purity 0.45 and total ploidy 1.60...
INFO [2025-08-17 22:23:04] Recalibrating log-ratios...
INFO [2025-08-17 22:23:04] Testing local optimum 16/19 at purity 0.45 and total ploidy 1.60...
INFO [2025-08-17 22:23:04] Testing local optimum 17/19 at purity 0.62 and total ploidy 2.10...
INFO [2025-08-17 22:23:05] Testing local optimum 18/19 at purity 0.78 and total ploidy 2.00...
INFO [2025-08-17 22:23:05] Testing local optimum 19/19 at purity 0.62 and total ploidy 1.40...
INFO [2025-08-17 22:23:05] Recalibrating log-ratios...
INFO [2025-08-17 22:23:05] Testing local optimum 19/19 at purity 0.62 and total ploidy 1.40...
INFO [2025-08-17 22:23:06] Recalibrating log-ratios...
INFO [2025-08-17 22:23:06] Testing local optimum 19/19 at purity 0.62 and total ploidy 1.40...
INFO [2025-08-17 22:23:06] Recalibrating log-ratios...
INFO [2025-08-17 22:23:06] Testing local optimum 19/19 at purity 0.62 and total ploidy 1.40...
INFO [2025-08-17 22:23:06] Skipping 5 solutions that converged to the same optima.
INFO [2025-08-17 22:23:06] Skipping 7 solutions exceeding max.non.clonal (0.20): 0.37/0.83, 0.45/0.68, 0.62/6.1, 0.45/1.26, 0.64/0.63, 0.48/0.89, 0.64/0.88 (purity/tumor ploidy)
INFO [2025-08-17 22:23:06] Fitting variants with beta model for local optimum 4/19...
INFO [2025-08-17 22:23:06] Fitting variants for purity 0.32, tumor ploidy 1.40 and contamination 0.01.
INFO [2025-08-17 22:23:10] Rare karyotype solution. Skipping post-optimization.
INFO [2025-08-17 22:23:10] Optimized purity: 0.32
INFO [2025-08-17 22:23:10] Fitting variants with beta model for local optimum 7/19...
INFO [2025-08-17 22:23:10] Fitting variants for purity 0.19, tumor ploidy 1.40 and contamination 0.01.
INFO [2025-08-17 22:23:14] Rare karyotype solution. Skipping post-optimization.
INFO [2025-08-17 22:23:14] Optimized purity: 0.19
INFO [2025-08-17 22:23:14] Fitting variants with beta model for local optimum 13/19...
INFO [2025-08-17 22:23:14] Fitting variants for purity 0.39, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:19] Fitting variants for purity 0.35, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:23] Fitting variants for purity 0.36, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:27] Fitting variants for purity 0.37, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:31] Fitting variants for purity 0.38, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:34] Fitting variants for purity 0.40, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:38] Fitting variants for purity 0.41, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:42] Fitting variants for purity 0.42, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:46] Fitting variants for purity 0.43, tumor ploidy 2.85 and contamination 0.01.
INFO [2025-08-17 22:23:50] Optimized purity: 0.35
INFO [2025-08-17 22:23:50] Fitting variants with beta model for local optimum 14/19...
INFO [2025-08-17 22:23:50] Fitting variants for purity 0.55, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:23:54] Fitting variants for purity 0.51, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:23:57] Fitting variants for purity 0.52, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:01] Fitting variants for purity 0.53, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:05] Fitting variants for purity 0.54, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:09] Fitting variants for purity 0.56, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:13] Fitting variants for purity 0.57, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:16] Fitting variants for purity 0.58, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:20] Fitting variants for purity 0.59, tumor ploidy 1.88 and contamination 0.01.
INFO [2025-08-17 22:24:24] Optimized purity: 0.51
INFO [2025-08-17 22:24:24] Fitting variants with beta model for local optimum 15/19...
INFO [2025-08-17 22:24:24] Fitting variants for purity 0.72, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:28] Fitting variants for purity 0.68, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:32] Fitting variants for purity 0.69, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:36] Fitting variants for purity 0.70, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:40] Fitting variants for purity 0.71, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:44] Fitting variants for purity 0.73, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:48] Fitting variants for purity 0.74, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:52] Fitting variants for purity 0.75, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:56] Fitting variants for purity 0.76, tumor ploidy 2.90 and contamination 0.01.
INFO [2025-08-17 22:24:59] Optimized purity: 0.68
INFO [2025-08-17 22:24:59] Fitting variants with beta model for local optimum 17/19...
INFO [2025-08-17 22:24:59] Fitting variants for purity 0.42, tumor ploidy 1.41 and contamination 0.01.
INFO [2025-08-17 22:25:03] Rare karyotype solution. Skipping post-optimization.
INFO [2025-08-17 22:25:03] Optimized purity: 0.42
INFO [2025-08-17 22:25:03] Fitting variants with beta model for local optimum 18/19...
INFO [2025-08-17 22:25:03] Fitting variants for purity 0.72, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:07] Fitting variants for purity 0.68, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:11] Fitting variants for purity 0.69, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:15] Fitting variants for purity 0.70, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:18] Fitting variants for purity 0.71, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:22] Fitting variants for purity 0.73, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:26] Fitting variants for purity 0.74, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:30] Fitting variants for purity 0.75, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:34] Fitting variants for purity 0.76, tumor ploidy 1.99 and contamination 0.01.
INFO [2025-08-17 22:25:37] Optimized purity: 0.68
INFO [2025-08-17 22:25:37] Done.
INFO [2025-08-17 22:25:37] ------------------------------------------------------------
Warning message:
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
INFO [2025-08-17 22:25:38] Generating output files...
Warning messages:
1: In par(par.mar) : argument 1 does not name a graphical parameter
2: In par(par.mar) : argument 1 does not name a graphical parameter
3: In par(par.mar) : argument 1 does not name a graphical parameter
4: In par(par.mar) : argument 1 does not name a graphical parameter
5: In par(par.mar) : argument 1 does not name a graphical parameter
6: In par(par.mar) : argument 1 does not name a graphical parameter
7: In par(par.mar) : argument 1 does not name a graphical parameter
Error in if (opt$out_vcf) { : missing value where TRUE/FALSE needed
Execution halted
Could you please advise what might be causing this issue and how I can improve it?
Here is an example of the overall run output:
Thank you for your attention and assistance.

[HuZhuocheng]

I think I have compromised. I removed the --out-vcf parameter. However, the issue I am more concerned about is that in the ID_genes.csv of my results, the type of most samples is NA. Many samples even have all values as NA or DELETION, while the Amplication (Note: The correct spelling in genetics is usually "Amplification") is missing. Let me take one sample as an example: this gene has the highest gene.mean (1.753) among all genes in this sample, but its type is NA:

IGHV3-23 chr14 106268526 106268733 0.794882814 NA -0.44047422 66 1 1.753 1.753 1.753 FALSE 0 NA 3 0 TRUE TRUE

I checked this locus in IGV (Integrative Genomics Viewer), [upper is normal sample] and it really looks like an Amplication to me.

[HuZhuocheng]

My sample is a DLBCL (diffuse large B-cell lymphoma) sample, but the tumor purity obtained from the sample is around 0.6, which seems much lower than expected. I would like to ask if there are any testing or improvement methods.

[lima1]

Hi @HuZhuocheng ,

can you try the latest stable version? And then I would recommend following the best practices https://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/Quick.html, ideally also using the internal normalization and PSCBS segmentation.

You can then compare the CNVkit results. PureCN does not work without process matched normal samples. You also only have 8% of intervals covered by SNPs. It should be around 15% for hybrid capture assays with 50-75bp padding. Is this a PCR assay?

Markus