diff --git a/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam new file mode 100644 index 000000000..3ec8b77a8 Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam differ diff --git a/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai new file mode 100644 index 000000000..7e74caeab Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_genotype.bam.bai differ diff --git a/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz new file mode 100644 index 000000000..e2891148e Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz differ diff --git a/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz.tbi b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz.tbi new file mode 100644 index 000000000..a1e42c0f2 Binary files /dev/null and b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/HG002_ont_sv_sites.vcf.gz.tbi differ diff --git a/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/README.md b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/README.md new file mode 100644 index 000000000..0c123c6fe --- /dev/null +++ b/data/genomics/homo_sapiens/nanopore/bam/HG002_ont_sv_genotype/README.md @@ -0,0 +1,25 @@ +# HG002 ONT SV genotyping test data + +Small BAM and a VCF of known structural variants (SVs), for testing SV genotyping tools that genotype a given set of SVs in a long-read alignment (e.g. Sniffles `--genotype-vcf`). + +- **Source**: GIAB HG002 ONT reads, R10.4.1 flowcell (PAW70337), HAC basecalling (`dna_r10.4.1_e8.2_400bps_hac@v5.0.0`), aligned to GRCh38 (chr-prefixed contigs) +- **Regions**: four windows of 1-5 kb on chr2, chr7, chr9 and chr18, containing heterozygous deletions, an insertion cluster, homozygous deletions and a heterozygous inversion +- **Downsampled**: whole reads kept by read-name hash (`samtools view -M -s 42.`) to ~12x in the windows +- **Cleaned**: base qualities set to `*`; `MM`, `ML`, `mv`, `ts`, `ns`, `HP` and `PS` tags, `@PG` lines and `UR` paths removed + +## Files + +| File | Size | Description | +| ------------------------------- | -------- | ---------------------------------------------------------- | +| `HG002_ont_sv_genotype.bam` | ~0.77 MB | Coordinate-sorted reads of the four windows | +| `HG002_ont_sv_genotype.bam.bai` | ~162 KB | BAM index | +| `HG002_ont_sv_sites.vcf.gz` | ~3 KB | 15 SV records of HG002 in the windows (INS, DEL, INV, BND) | +| `HG002_ont_sv_sites.vcf.gz.tbi` | <1 KB | VCF index | + +## Sites VCF + +SV records called on HG002 with long-read SV callers and merged. Each record carries `SVTYPE`, `END`, `SVLEN` (and `CHR2` where present) and the callers' `GT` for HG002 (some `./.`). `QUAL` is `.`, `` records and records longer than 100 kb are not included. + +## Expected genotypes + +Genotyping the VCF on the BAM with Sniffles 2.8.1 (`sniffles --input --genotype-vcf --vcf `) gives 1 `0/0`, 7 `0/1` and 7 `1/1`.