Result files¶
The pipeline generates many files, but only specific ones are defined as final outputs. These are configured in config/output_files_FFPE.yaml and config/output_files_ctDNA.yaml.
{sample} is replaced with the sample name and {type} is replaced with the sample type (T/N/R, where T=Tumor, N=Normal, R=RNA).
FFPE Pipeline Output¶
Files defined in output_files_FFPE.yaml.
DNA¶
Alignment¶
| File | Description |
|---|---|
bam_dna/{sample}_{type}.bam |
BAM |
bam_dna/{sample}_{type}.bam.bai |
BAM index |
bam_dna/mutect2_indel_bam/{sample}_{type}.bam |
Mutect2 INDEL BAM |
bam_dna/mutect2_indel_bam/{sample}_{type}.bam.bai |
Mutect2 INDEL BAM index |
SNV and INDELs¶
| File | Description |
|---|---|
gvcf_dna/{sample}_{type}.mosdepth.g.vcf.gz |
Mosdepth GVCF |
results/dna/{sample}_{type}/additional_files/vcf/{sample}_{type}.annotated.vcf.gz |
Vep annotated VCF |
results/dna/{sample}_{type}/additional_files/vcf/{sample}_{type}.annotated.exon_only.filter.soft_filter.vcf |
Exon-only soft-filtered VCF |
results/dna/{sample}_{type}/additional_files/vcf/{sample}_{type}.annotated.exon_only.filter.hard_filter.vcf |
Exon-only hard-filtered VCF |
results/dna/{sample}_{type}/vcf/{sample}_{type}.annotated.exon_only.filter.hard_filter.codon_snv.vcf |
Codon SNV VCF |
results/dna/{sample}_{type}/vcf/{sample}_{type}.annotated.exon_only.filter.hard_filter.codon_snv.qci.vcf |
QCI VCF |
results/dna/{sample}_{type}/additional_files/vcf/{caller}_{sample}_{type}.vcf.gz |
Caller VCF |
results/dna/{sample}_{type}/id_snps/{sample}_{type}.id_snps.vcf |
ID-SNP VCF DNA |
QC¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.duplication_metrics.txt |
Duplication metrics |
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.alignment_summary_metrics.txt |
Alignment summary metrics |
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.HsMetrics.txt |
HsMetrics |
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.insert_size_metrics.txt |
Insert size metrics |
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.samtools-stats.txt |
Samtools stats |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.tsv |
Coverage and mutations all |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.ENC.tsv |
Coverage and mutations ENC |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.URO.tsv |
Coverage and mutations URO |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.BRC.tsv |
Coverage and mutations BRC |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.CRC.tsv |
Coverage and mutations CRC |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.GIS.tsv |
Coverage and mutations GIS |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.LUN.tsv |
Coverage and mutations LUN |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.MEL.tsv |
Coverage and mutations MEL |
results/dna/{sample}_{type}/qc/{sample}_{type}.coverage_and_mutations.TYR.tsv |
Coverage and mutations TYR |
results/dna/{sample}_{type}/additional_files/qc/{sample}_{type}.contamination.table |
Contamination table |
results/dna/qc/multiqc_DNA.html |
MultiQC DNA HTML |
Reports¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/{sample}_{type}.general_report.html |
Results report DNA HTML |
results/dna/{sample}_{type}/{sample}_{type}.prio.general_report.html |
Results report small panel DNA HTML |
Biomarker¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/biomarker/{sample}_{type}.msisensor_pro.filtered.score.tsv |
MSI Sensor Pro filtered TSV |
results/dna/{sample}_{type}/biomarker/{sample}_{type}.msisensor_pro.unfiltered.score.tsv |
MSI Sensor Pro unfiltered TSV |
results/dna/{sample}_{type}/biomarker/{sample}_{type}.TMB.txt |
TMB |
results/dna/{sample}_{type}/additional_files/biomarker/{sample}_{type}.purecn.scarhrd_cnvkit_score.txt |
HRD score - PureCN |
results/dna/{sample}_{type}/additional_files/biomarker/{sample}_{type}.pathology.scarhrd_cnvkit_score.txt |
HRD score - pathology |
results/dna/{sample}_{type}/biomarker/{sample}_{type}.pathology_purecn.scarhrd_cnvkit_score.txt |
HRD score - pathology_purecn |
results/dna/{sample}_{type}/biomarker/{sample}_{type}.pathology_purecn.predicted_gis.txt |
Predicted GIS score |
Fusions¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/fusion/{sample}_{type}.fuseq_wes.report.csv |
fuseq WES |
results/dna/{sample}_{type}/additional_files/fusion/{sample}_{type}.fuseq_wes.unfiltered.results.csv |
fuseq WES unfiltered |
results/dna/{sample}_{type}/fusion/{sample}_{type}.juli.filtered.fusions.txt |
JuLI fusions |
results/dna/{sample}_{type}/additional_files/fusion/{sample}_{type}.juli.fusions.txt |
JuLI unfiltered fusions |
CNV¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.cnvkit.scatter.png |
CNVkit scatter PNG |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.cnvkit.diagram.pdf |
CNVkit diagram PDF |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.purecn.svdb_query.vcf |
SVDB query - PureCN |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology.svdb_query.vcf |
SVDB query - pathology |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology_purecn.svdb_query.vcf |
SVDB query - pathology_purecn |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.purecn.cnv.html |
CNV HTML report - PureCN |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology.cnv.html |
CNV HTML report - pathology |
results/dna/{sample}_{type}/cnv/{sample}_{type}.pathology_purecn.cnv.html |
CNV HTML report - pathology_purecn |
results/dna/{sample}_{type}/cnv/{sample}_{type}.purecn_purity_ploidity.csv |
PureCN purity |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.purecn.amp_all_del_all.cnv_report.tsv |
CNV TSV report - PureCN |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology.amp_all_del_all.cnv_report.tsv |
CNV TSV report - pathology |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology_purecn.amp_all_del_all.cnv_report.tsv |
CNV TSV report - pathology_purecn |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.purecn.amp_all_del_validated.cnv_report.tsv |
CNV TSV report validated - PureCN |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology.amp_all_del_validated.cnv_report.tsv |
CNV TSV report validated - pathology |
results/dna/{sample}_{type}/cnv/{sample}_{type}.pathology_purecn.amp_all_del_validated.cnv_report.tsv |
CNV TSV report validated - pathology_purecn |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.deletions.tsv |
Small CNV deletions |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.amplifications.tsv |
Small CNV amplifications |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology.jumble.vcf |
Jumble vcf pathology |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.purecn.jumble.vcf |
Jumble vcf purecn |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.pathology_purecn.jumble.vcf |
Jumble vcf pathology_purecn |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.germline.vcf.gz |
Germline vcf used in CNV analysis |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.manta_tumorSV.vcf.gz |
Manta VCF |
results/dna/{sample}_{type}/cnv/{sample}_{type}.ctDNA_fraction.tsv |
ctDNA fraction |
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.ctDNA_fraction_info.tsv |
ctDNA fraction_info |
results/dna/{sample}_{type}/cnv/{sample}_{type}.ITD.hard_filter.vcf |
ITD filtered |
RNA¶
Alignment¶
| File | Description |
|---|---|
bam_rna/{sample}_{type}.star_fusion.bam |
STAR Fusion BAM |
bam_rna/{sample}_{type}.star_fusion.bam.bai |
STAR Fusion BAM index |
SNV and INDELs¶
| File | Description |
|---|---|
results/rna/{sample}_{type}/id_snps/{sample}_{type}.id_snps.vcf |
ID-SNP VCF RNA |
QC¶
| File | Description |
|---|---|
results/rna/{sample}_{type}/qc/{sample}_{type}.house_keeping_gene_coverage.tsv |
Housekeeping gene coverage |
results/rna/qc/multiqc_RNA.html |
MultiQC RNA HTML |
results/sample_mixup_check.tsv |
RNA DNA sample mixup report |
Fusions¶
| File | Description |
|---|---|
results/rna/{sample}_{type}/fusion/{sample}_{type}.fusion_report.tsv |
Fusion report TSV |
results/rna/{sample}_{type}/additional_files/fusion/{sample}_{type}.arriba.fusions.tsv |
Arriba fusion TSV |
results/rna/{sample}_{type}/fusion/{sample}_{type}.arriba.fusions.pdf |
Arriba fusion PDF |
results/rna/{sample}_{type}/fusion/{sample}_{type}.exon_skipping.tsv |
Exon skipping TSV |
results/rna/{sample}_{type}/additional_files/fusion/{sample}_{type}.ctat.exon_skipping.unfiltered.tsv |
CTAT-splicing unfiltered TSV |
results/rna/{sample}_{type}/fusion/{sample}_{type}.ctat.exon_skipping.filtered.tsv |
CTAT-splicing filtered TSV |
results/rna/{sample}_{type}/fusion/{sample}_{type}.ctat.exon_skipping.igv.html |
CTAT-splicing html |
results/rna/{sample}_{type}/additional_files/fusion/{sample}_{type}.star-fusion.fusion_predictions.tsv |
STAR Fusion prediction TSV |
results/rna/{sample}_{type}/additional_files/fusion/{sample}_{type}.fusioncatcher.fusion_predictions.txt |
Fusioncatcher prediction TSV |
ctDNA Pipeline Output¶
Files defined in output_files_ctDNA.yaml that differ or are specific to ctDNA.
Alignment¶
| File | Description |
|---|---|
bam_dna/{sample}_{type}.umi.bam |
BAM umi |
bam_dna/{sample}_{type}.umi.bam.bai |
BAM umi index |
SNV and INDELs¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/additional_files/vcf/{sample}_{type}.annotated.exon_only.filter.soft_filter.umi.vcf |
Exon-only soft-filtered VCF UMI |
results/dna/{sample}_{type}/vcf/{sample}_{type}.annotated.exon_only.filter.hard_filter.codon_snv.umi.qci.vcf |
QCI umi VCF |
Reports¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/{sample}_{type}.umi.general_report.html |
Results report umi DNA HTML |
Biomarker¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/biomarker/{sample}_{type}.umi.TMB.txt |
TMB umi |
results/dna/{sample}_{type}/hla/{sample}_{type}_hla_type_result.tsv |
HLA optitype |
results/dna/{sample}_{type}/hla/{sample}_{type}_hla_type_coverage_plot.pdf |
HLA coverage optitype |
Fusions¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/fusion/{sample}_{type}.gene_fuse_report.umi.tsv |
GeneFuse report |
results/dna/{sample}_{type}/additional_files/fusion/{sample}_{type}.gene_fuse.unfiltered.results.txt |
GeneFuse fusions unfiltered |
CNV¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/additional_files/cnv/{sample}_{type}.ITD.vcf |
ITD |
Fragmentomics¶
| File | Description |
|---|---|
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.end-motifs.tsv |
Fragmentomics end-motifs |
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.mds.txt |
Fragmentomics mds |
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.interval-end-motifs.tsv |
Fragmentomics interval-end-motifs |
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.interval-mds.txt |
Fragmentomics interval-mds |
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.frag-length-bins.tsv |
Fragmentomics fragment length bins |
results/dna/{sample}_{type}/fragmentomics/{sample}_{type}.fragment_length_score.txt |
Fragmentomics fragment length score |