--without-phasing mode: vcf_output missing despite bed_output being generated and no ploidy/purity estimation

[sandratra-rab]

Hi,
I am running Wakhan (0.4.2) in --without-phasing mode (mouse tumor genome, as suggested in the README).

python ${WAKHAN} all \
    --threads 16 \
    --target-bam ${TARGET_BAM} \
    --normal-phased-vcf ${NORMAL_VCF} \
    --breakpoints ${SV} \
    --genome-name ${COMPARISON_NAME} \
    --out-dir-plots ${OUTDIR} \
    --reference ${REF} \
    --centromere ${CENTROMERES} \
    --cancer-genes ${GENES_OF_INTEREST} \
    --contigs 1-19,X,Y \
    --loh-enable \
    --without-phasing

Observed behavior

In --without-phasing mode:

• bed_output/ is generated, CNA segments are computed
• vcf_output/ is not generated
• No ploidy/purity estimation in HTML plot titles

Output directory:

Wakhan_unphased/SAMPLE-TUMOR_vs_SAMPLE-NORMAL/
├── bed_output
│   ├── SAMPLE-TUMOR_vs_SAMPLE-NORMAL_copynumbers_segments.bed
│   └── SAMPLE-TUMOR_vs_SAMPLE-NORMAL_copynumbers_subclonal_segments.bed
├── coverage_data
│   ├── baf.csv
│   ├── cn_coverage.png
│   ├── cn_peaks.png
│   └── coverage.csv
├── coverage_plots
│   ├── 10_cov.html
│   ├── 11_cov.html
│   ├── 12_cov.html
│   ├── 13_cov.html
│   ├── 14_cov.html
│   ├── 15_cov.html
│   ├── 16_cov.html
│   ├── 17_cov.html
│   ├── 18_cov.html
│   ├── 19_cov.html
│   ├── 1_cov.html
│   ├── 2_cov.html
│   ├── 3_cov.html
│   ├── 4_cov.html
│   ├── 5_cov.html
│   ├── 6_cov.html
│   ├── 7_cov.html
│   ├── 8_cov.html
│   ├── 9_cov.html
│   ├── COVERAGE_INDEX.html
│   ├── X_cov.html
│   └── Y_cov.html
├── SAMPLE-TUMOR_vs_SAMPLE-NORMAL_genome_copynumbers_breakpoints.html
├── SAMPLE-TUMOR_vs_SAMPLE-NORMAL_genome_copynumbers_breakpoints_subclonal.html
├── SAMPLE-TUMOR_vs_SAMPLE-NORMAL_genome_copynumbers_details.html
├── phasing_output
│   ├── 10_phase_correction_1.html
│   ├── 10_phase_correction_2.html
│   ├── 10_without_phase_correction.html
│   ├── 11_phase_correction_0.1.html
│   ├── 11_phase_correction_0.2.html
│   ├── 11_phase_correction_0.3.html
│   ├── 11_phase_correction_1.html
│   ├── 11_phase_correction_2.html
│   ├── 11_without_phase_correction.html
│   ├── 12_phase_correction_0.1.html
│   ├── 12_phase_correction_0.2.html
│   ├── 12_phase_correction_0.3.html
│   ├── 12_phase_correction_1.html
│   ├── 12_phase_correction_2.html
│   ├── 12_without_phase_correction.html
│   ├── 13_phase_correction_0.1.html
│   ├── 13_phase_correction_0.2.html
│   ├── 13_phase_correction_0.3.html
│   ├── 13_phase_correction_1.html
│   ├── 13_phase_correction_2.html
│   ├── 13_without_phase_correction.html
│   ├── 14_phase_correction_1.html
│   ├── 14_phase_correction_2.html
│   ├── 14_without_phase_correction.html
│   ├── 15_phase_correction_0.1.html
│   ├── 15_phase_correction_0.2.html
│   ├── 15_phase_correction_0.3.html
│   ├── 15_phase_correction_1.html
│   ├── 15_phase_correction_2.html
│   ├── 15_without_phase_correction.html
│   ├── 16_phase_correction_0.1.html
│   ├── 16_phase_correction_0.2.html
│   ├── 16_phase_correction_0.3.html
│   ├── 16_phase_correction_1.html
│   ├── 16_phase_correction_2.html
│   ├── 16_without_phase_correction.html
│   ├── 17_phase_correction_1.html
│   ├── 17_phase_correction_2.html
│   ├── 17_without_phase_correction.html
│   ├── 18_phase_correction_1.html
│   ├── 18_phase_correction_2.html
│   ├── 18_without_phase_correction.html
│   ├── 19_phase_correction_0.1.html
│   ├── 19_phase_correction_0.2.html
│   ├── 19_phase_correction_0.3.html
│   ├── 19_phase_correction_1.html
│   ├── 19_phase_correction_2.html
│   ├── 19_without_phase_correction.html
│   ├── 1_phase_correction_0.1.html
│   ├── 1_phase_correction_0.2.html
│   ├── 1_phase_correction_0.3.html
│   ├── 1_phase_correction_1.html
│   ├── 1_phase_correction_2.html
│   ├── 1_without_phase_correction.html
│   ├── 2_phase_correction_0.1.html
│   ├── 2_phase_correction_0.2.html
│   ├── 2_phase_correction_0.3.html
│   ├── 2_phase_correction_1.html
│   ├── 2_phase_correction_2.html
│   ├── 2_without_phase_correction.html
│   ├── 3_phase_correction_0.1.html
│   ├── 3_phase_correction_0.2.html
│   ├── 3_phase_correction_0.3.html
│   ├── 3_phase_correction_1.html
│   ├── 3_phase_correction_2.html
│   ├── 3_without_phase_correction.html
│   ├── 4_phase_correction_0.1.html
│   ├── 4_phase_correction_0.2.html
│   ├── 4_phase_correction_0.3.html
│   ├── 4_phase_correction_1.html
│   ├── 4_phase_correction_2.html
│   ├── 4_without_phase_correction.html
│   ├── 5_phase_correction_0.1.html
│   ├── 5_phase_correction_0.2.html
│   ├── 5_phase_correction_0.3.html
│   ├── 5_phase_correction_1.html
│   ├── 5_phase_correction_2.html
│   ├── 5_without_phase_correction.html
│   ├── 6_phase_correction_1.html
│   ├── 6_phase_correction_2.html
│   ├── 6_without_phase_correction.html
│   ├── 7_phase_correction_1.html
│   ├── 7_phase_correction_2.html
│   ├── 7_without_phase_correction.html
│   ├── 8_phase_correction_0.1.html
│   ├── 8_phase_correction_0.2.html
│   ├── 8_phase_correction_0.3.html
│   ├── 8_phase_correction_1.html
│   ├── 8_phase_correction_2.html
│   ├── 8_without_phase_correction.html
│   ├── 9_phase_correction_0.1.html
│   ├── 9_phase_correction_0.2.html
│   ├── 9_phase_correction_0.3.html
│   ├── 9_phase_correction_1.html
│   ├── 9_phase_correction_2.html
│   ├── 9_without_phase_correction.html
│   ├── PHASE_CORRECTION_INDEX.html
│   ├── rephased.vcf.gz
│   ├── rephased.vcf.gz.csi
│   ├── X_phase_correction_0.1.html
│   ├── X_phase_correction_0.2.html
│   ├── X_phase_correction_0.3.html
│   ├── X_phase_correction_1.html
│   ├── X_phase_correction_2.html
│   ├── X_without_phase_correction.html
│   ├── Y_phase_correction_1.html
│   ├── Y_phase_correction_2.html
│   └── Y_without_phase_correction.html
└── wakhan.log

4 directories, 140 files

Feature request

• Would it be possible to generate a vcf_output/ even in --without-phasing mode, using a simplified (non haplotype specific) schema segments (e.g I suppose a VCF conversion of the already generated BED) ?
• The absence of vcf_output/ and ploidy/purity in unphased mode is not documented anywhere in the README. If it is intended, could this be clarified in the README ?

Thank you for your help.