Variant discovery and callable-region characterization for the Clarias gariepinus hatchery cohort (n = 226):
- biallelic SNPs (ANGSD genotype likelihoods, Beagle GL format)
- callable mask
- small variants (clair3, per-sample VCF)
- structural variants (DELLY + Manta, dual-caller validation)
This is one of three sibling catfish-{population,diversity,variant}-analysis
repos that together produce the population-genetic primitives consumed by
inversion-atlas and any future
papers on this cohort.
The variant data layer that everything else is built on:
| Output | Description | Consumed by |
|---|---|---|
| Callable-site mask (BED) | per-position pass/fail across the cohort | diversity, population, this repo |
| biSNP set (Beagle GL) | MAF ≥ 0.05, biallelic, thinned variants | population (PCA, NGSadmix), diversity (ROH) |
| SNP majmin assignments by RF | major/minor allele orientation per RF | population (Beagle subsets) |
| clair3 small-variant VCFs | per-sample, hard-genotyped | inversion-atlas (GHSL haplotype matrix) |
| DELLY SV calls | DEL / DUP / INV / BND / TRA / INS, per-sample | inversion-atlas (SV evidence layer) |
| Manta SV calls | dual-caller corroboration | inversion-atlas (SV evidence layer) |
| Dual-caller breakpoint-validated SV set | DELLY ∩ Manta | inversion-atlas |
| Input | From |
|---|---|
| BAMs + BAI | upstream read prep (currently ${BASE}/01-bams/ on LANTA) |
| Reference FASTA | ${BASE}/00-samples/fClaHyb_Gar_LG.fa |
| Sample manifest | ${BASE}/01_inputs_check/ |
- ANGSD (system) — biSNP discovery via genotype likelihoods
angsd_fixed_HWE— patched ANGSD with fixed-F EM (used where standard HWE-based MAF estimation gives biased calls in the family-structured hatchery cohort)- clair3 (system) — small-variant calling
- DELLY2 (system) — SV calling, primary
- Manta (system) — SV calling, secondary / corroborator
- bcftools, samtools, bedtools (system)
catfish-variant-analysis/
├── 00_config.sh root config
├── Modules/
│ ├── 01_callable_mask/ per-cohort callable-site BED
│ ├── 02_biSNP_discovery/ ANGSD biallelic SNP set + Beagle GLs
│ ├── 03_clair3/ small-variant calling per sample
│ ├── 04_sv_delly/ DELLY DEL/DUP/INV/BND/TRA/INS
│ ├── 05_sv_manta/ Manta SV calls
│ └── 06_sv_dual_validation/ DELLY ∩ Manta breakpoint validation
├── envs/
├── docs/
│ ├── module_contracts/
│ └── methods/
├── tests/
└── README.md
Scaffold. Pipelines exist on LANTA but live outside any git repo today
(spread across ${BASE}/popstruct_thin/04_beagle_byRF_majmin/,
${BASE}/03-variant-calls/, etc). They will be migrated into Modules/
over time, one module at a time.
Project umbrella DOI: TBD (Zenodo, will be issued at v1.0 tag).
This repo is for the 226-sample pure Clarias gariepinus hatchery cohort only. Do not use it for the F₁ hybrid (C. gariepinus × C. macrocephalus) genome assembly cohort or any future C. macrocephalus wild cohort — those are separate manuscripts and may need different parameter choices.