Analyze your own whole genome sequencing (WGS) data on consumer hardware. 33 default analysis steps (+ 1 opt-in somatic), all running locally in Docker.
| # | Step | Doc |
|---|---|---|
| 1 | ORA to FASTQ (Illumina decompression) | 01-ora-to-fastq.md |
| 1b | fastp QC + Trimming | 01b-fastp-qc.md |
| 2 | Alignment (minimap2 + samtools) | 02-alignment.md |
| 3 | Variant Calling (DeepVariant) | 03-variant-calling.md |
| 4 | Structural Variants (Manta) | 04-structural-variants.md |
| 5 | SV Annotation (AnnotSV) | 05-annotsv.md |
| 6 | ClinVar Screen | 06-clinvar-screen.md |
| 7 | Pharmacogenomics (PharmCAT) | 07-pharmacogenomics.md |
| 8 | HLA Typing (T1K) | 08-hla-typing.md |
| 9 | STR Expansions (ExpansionHunter) | 09-str-expansions.md |
| 10 | Telomere Length (TelomereHunter) | 10-telomere-analysis.md |
| 11 | ROH Analysis (bcftools roh) | 11-roh-analysis.md |
| 12 | Mito Haplogroup (haplogrep3) | 12-mito-haplogroup.md |
| 13 | VEP Annotation | 13-vep-annotation.md |
| 14 | Imputation Prep | 14-imputation-prep.md |
| 15 | SV Quality (duphold) | 15-duphold.md |
| 16 | Coverage QC (indexcov) | 16-indexcov.md |
| 16b | Coverage Statistics (mosdepth) | 16b-mosdepth.md |
| 17 | Cancer Predisposition (CPSR) | 17-cpsr.md |
| 18 | CNV Calling (CNVnator) | 18-cnvnator.md |
| 19 | SV Calling (Delly) | 19-delly.md |
| 20 | Mitochondrial (GATK Mutect2) | 20-mtoolbox.md |
| # | Step | Doc |
|---|---|---|
| 21 | CYP2D6 Star Alleles (Cyrius) | 21-cyrius.md |
| 22 | SV Consensus Merge | 22-survivor-merge.md |
| 23 | Clinical Variant Filter | 23-clinical-filter.md |
| 24 | HTML Summary Report | 24-html-report.md |
| 25 | Polygenic Risk Scores | 25-prs.md |
| 26 | Ancestry PCA | 26-ancestry.md |
| 27 | CPIC Drug Recommendations | 27-cpic-lookup.md |
| 28 | MultiQC Aggregation | 28-multiqc.md |
| 29 | Somatic Variants (Mutect2) | 29-mutect2-somatic.md |
| 30 | Annotation Enrichment (vcfanno) | 30-vcfanno.md |
| 31 | Variant Prioritization (slivar) | 31-slivar.md |
| 32 | Pharmacogenomics (pypgx) | 32-pypgx.md |