Outputs

CBIcall writes each run into a run directory named from the workflow choices:

cbicall_<engine>_<pipeline>_<mode>_<genome>_<gatk-version>_<run-id>/

The exact files depend on the selected pipeline and mode. The tables below are derived from the workflow output definitions and the checked-in example runs.

Most users only need these

• WES/WGS: use the final QC VCF in 02_varcall/.
• WES/WGS single-sample runs: keep the gVCF if you plan cohort joint genotyping.
• mtDNA: use 01_mtoolbox/mit_prioritized_variants.txt and the browser report in 02_browser/.

Common Run Files

File	Meaning
log.json	Structured record of CLI arguments, resolved configuration, selected profile, compact resources.bundle provenance, and runtime parameters.
run-report.json	Compact audit report with CBIcall version, status, elapsed time, workflow file fingerprints, resource fingerprint, output fingerprints when available, and workflow log path.
<engine>_<pipeline>_<mode>_<genome>_<gatk-version>.log	Main wrapper log for Bash runs.
logs/*.log	Per-rule or per-step logs for Snakemake/GATK 4.6 workflows.

Use config.resources.bundle.fingerprint inside log.json to check whether two runs used the same declared external dependency set.

Use workflow.fingerprint inside run-report.json to check whether two runs used the same resolved workflow file contents. If the fingerprint differs, inspect workflow.files to see which entrypoint, helper, Snakefile, or config file changed. WES/WGS single-sample runs also include parsed VCF hash reports under outputs.vcf_hash_reports when 03_stats/*.vcf.sha256.txt is present.

Two runs can be compared directly:

bin/cbicall compare-runs run_a/ run_b/ run_c/ --output compare-report.txt --html compare-report.html

The text report is the audit artifact. The optional HTML report renders the same information for browsing. See Run Comparison for details and an example screenshot.

WES/WGS Single-Sample

Applies to pipeline: wes or pipeline: wgs with mode: single.

Recommended Files

File	Use
02_varcall/<id>.hc.QC.vcf.gz	Final filtered single-sample VCF. This is the primary workflow VCF for downstream tools or review.
02_varcall/<id>.hc.QC.vcf.gz.tbi	Tabix index for the final VCF.
02_varcall/<id>.hc.g.vcf.gz	Per-sample gVCF. Use this as input for cohort joint genotyping.
02_varcall/<id>.hc.g.vcf.gz.tbi	Tabix index for the gVCF.
03_stats/<id>.coverage.txt	Coverage summary.
03_stats/<id>.sex.txt	Sex inference result from the final VCF.

Intermediate files

File	Meaning
01_bam/<fastq-prefix>.rg.bam	Lane-level BAM after alignment and read-group assignment.
01_bam/<id>.rg.merged.bam	BAM after merging lanes for the sample.
01_bam/<id>.rg.merged.dedup.bam	Duplicate-marked BAM.
01_bam/<id>.rg.merged.dedup.metrics.txt	Duplicate-marking metrics.
01_bam/<id>.rg.merged.dedup.recal.table	BQSR recalibration table.
01_bam/<id>.rg.merged.dedup.recal.bam	Recalibrated BAM used for variant calling.
01_bam/*.bai or 01_bam/*.bam.bai	BAM indexes.
02_varcall/<id>.hc.raw.vcf.gz	Raw VCF from GenotypeGVCFs.
02_varcall/<id>.hc.raw.vcf.gz.tbi	Tabix index for the raw VCF.

Conditional VQSR files

These appear only when the run has enough SNPs or indels to build VQSR models.

File	Meaning
02_varcall/<id>.hc.snp.recal.vcf.gz	SNP VQSR model output.
02_varcall/<id>.hc.snp.tranches.txt	SNP VQSR tranche diagnostics.
02_varcall/<id>.hc.post_snp.vcf.gz	VCF after applying SNP VQSR.
02_varcall/<id>.hc.indel.recal.vcf.gz	INDEL VQSR model output.
02_varcall/<id>.hc.indel.tranches.txt	INDEL VQSR tranche diagnostics.
02_varcall/<id>.hc.vqsr.vcf.gz	VCF after applying SNP and INDEL VQSR.

note

If VQSR is skipped because there are too few variants, the final *.hc.QC.vcf.gz is still produced by hard filtering.

WES/WGS Cohort

Applies to pipeline: wes or pipeline: wgs with mode: cohort.

Recommended Files

File	Use
02_varcall/cohort.gv.QC.vcf.gz	Final filtered cohort VCF. This is the primary joint-genotyped variant file.
02_varcall/cohort.gv.QC.vcf.gz.tbi	Tabix index for the final cohort VCF.

Intermediate files

File	Meaning
02_varcall/cohort.genomicsdb.<run-id>/	GenomicsDB workspace used by GenomicsDBImport.
02_varcall/genomicsdbimport.done	Snakemake marker showing that GenomicsDB import completed.
02_varcall/cohort.gv.raw.vcf.gz	Raw cohort VCF from GenotypeGVCFs.
02_varcall/cohort.gv.raw.vcf.gz.tbi	Tabix index for the raw cohort VCF.
logs/01_genomicsdbimport.log	GenomicsDB import log.
logs/02_genotype_gvcfs.log	Cohort genotyping log.
logs/03_vqsr_and_qc.log	VQSR and final filtering log.

Conditional VQSR files

File	Meaning
02_varcall/cohort.snp.recal.vcf.gz	SNP VQSR model output.
02_varcall/cohort.snp.tranches.txt	SNP VQSR tranche diagnostics.
02_varcall/cohort.post_snp.vcf.gz	VCF after applying SNP VQSR.
02_varcall/cohort.indel.recal.vcf.gz	INDEL VQSR model output.
02_varcall/cohort.indel.tranches.txt	INDEL VQSR tranche diagnostics.
02_varcall/cohort.vqsr.vcf.gz	VCF after applying SNP and INDEL VQSR.

mtDNA Single-Sample

Applies to pipeline: mit with mode: single.

Recommended Files

File	Use
01_mtoolbox/mit_prioritized_variants.txt	Final prioritized mtDNA variant report with GT, DP, and heteroplasmic fraction columns appended by CBIcall.
01_mtoolbox/VCF_file.vcf	mtDNA VCF from MToolBox.
02_browser/<run-id>.html	Interactive HTML report.
02_browser/mit.json	JSON used by the browser report.
02_browser/README.txt	Local instructions for opening the browser report.

Intermediate files

File	Meaning
01_mtoolbox/<id>-DNA_MIT.bam	Extracted mitochondrial BAM used as MToolBox input.
01_mtoolbox/<id>-DNA_MIT.bam.bai	BAM index.
01_mtoolbox/prioritized_variants.txt	Raw MToolBox prioritized variant list before CBIcall appends genotype/depth/HF fields.
01_mtoolbox/mit.raw.json	Raw JSON conversion of the final prioritized report.
01_mtoolbox/mt_classification_best_results.csv	MToolBox haplogroup/classification output.
01_mtoolbox/processed_fastq.tar.gz	MToolBox processed FASTQ archive.
01_mtoolbox/summary_*.txt	MToolBox run summary.
01_mtoolbox/OUT_*/	MToolBox working directory with alignment, pileup, coverage, and annotation intermediates.

mtDNA Cohort

Applies to pipeline: mit with mode: cohort.

The cohort workflow uses the same output directories as mtDNA single-sample mode, but extracts mtDNA BAMs from all matching sibling sample directories before running MToolBox jointly.

Recommended Files

File	Use
01_mtoolbox/mit_prioritized_variants.txt	Final joint mtDNA variant report with per-sample GT, DP, and heteroplasmic fraction fields.
01_mtoolbox/VCF_file.vcf	Joint mtDNA VCF from MToolBox.
02_browser/<run-id>.html	Interactive cohort HTML report.
02_browser/mit.json	JSON used by the browser report.
02_browser/README.txt	Local instructions for opening the browser report.

Intermediate files

File	Meaning
01_mtoolbox/<sample-id>-DNA_MIT.bam	Extracted mitochondrial BAM for each cohort sample.
01_mtoolbox/<sample-id>-DNA_MIT.bam.bai	BAM index for each extracted mitochondrial BAM.
01_mtoolbox/prioritized_variants.txt	Raw MToolBox prioritized variant list.
01_mtoolbox/missing_variants.txt	Temporary variant list used while appending cohort genotype/depth/HF fields.
01_mtoolbox/mit.raw.json	Raw JSON conversion of the final prioritized report.
01_mtoolbox/OUT_*/	MToolBox working directories and intermediate outputs.