Results files

The pipeline line generates lots of files of which only some are kept. These final output files are listed and shortly described in the table below. {sample} is replaced with the sample name and {type} with the sample type (e.g. T).

Main output files

File	File type	Description
Alignment
results/mapped_bam/pbmm2_align/{sample}_{type}.bam	BAM	Aligned reads (pbmm2)
results/mapped_bam/vacmap_align/{sample}_{type}.bam	BAM	Aligned reads (VACmap)
results/snv_indels/whatshap_haplotag/{sample}_{type}.haplotagged.bam	BAM	Haplotagged reads
results/snv_indels/whatshap_haplotag/{sample}_{type}.haplotagged.bam.bai	BAM index	Index for haplotagged reads
SNV & INDELs
results/snv_indels/whatshap_phase/{sample}_{type}.phased.include.panel.vep_annotated.vcf.gz	compressed VCF	Phased SNVs called by DeepSomatic or ClairS-TO, annotated by VEP
CNV & SV
results/cnv_sv/severus_t_only/{sample}_{type}_all_sv.include.panel.vcf.gz	compressed VCF	SVs called by Severus (tumor-only, haplotagged BAM)
results/cnv_sv/sniffles2/{sample}_{type}.include.panel.vcf.gz	compressed VCF	SVs called by Sniffles2
results/cnv_sv/pbsv_call/{sample}_{type}.include.panel.vcf.gz	compressed VCF	SVs called by PBSV
results/cnv_sv/svdb_merge/{sample}_{type}.vcf	VCF	Merged SV calls from all three callers (Severus, Sniffles2, PBSV)
results/cnv_sv/svdb_query/{sample}_{type}.vcf	VCF	Merged SVs annotated with population frequencies from the SVDB population database
results/cnv_sv/cnvkit/cnvkit_vcf/{sample}_{type}.pathology.annotate_cnv.germline.vcf.gz	compressed VCF	Annotated CNV calls from CNVkit
results/cnv_sv/cnvkit/cnvkit_batch/{sample}_{type}.cns	CNS	Copy number segments from CNVkit
results/cnv_sv/cnvkit/cnvkit_batch/{sample}_{type}.cnr	CNR	Copy number ratios from CNVkit
Depth of coverage
results/qc/mosdepth/{sample}_{type}.regions.bed.gz	compressed BED	Median depth of coverage per target region, generated by mosdepth
Reports
results/qc/multiqc/multiqc_design2.html	HTML	MultiQC report aggregating QC metrics
results/cnv_sv/cnvkit/html_reports/{sample}_{type}.pathology.cnv_report.html	HTML	Interactive CNV report generated by CNVkit
results/xlsx_reports/{sample}_{type}_combined_report.xlsx	XLSX	Excel report with SNV, SV, CNV variants of interest and a Software Versions tab