Working directory

Directory overview

The tree view of all subdirectories under your working directory ```reproduce_data````.

|-- CMRGs
|   |-- plat_compare
|   `-- stra_compare
|-- HiFi
|   |-- ExTD_hq_trio_validation
|   |-- lra_hifi_10kb
|   |   `-- raw_calls
|   |-- lra_hifi_15kb
|   |   `-- raw_calls
|   |-- lra_hifi_18kb
|   |   `-- raw_calls
|   |-- minimap2_hifi_10kb
|   |   `-- raw_calls
|   |-- minimap2_hifi_15kb
|   |   `-- raw_calls
|   |-- minimap2_hifi_18kb
|   |   `-- raw_calls
|   |-- ngmlr_hifi_10kb
|   |   `-- raw_calls
|   |-- ngmlr_hifi_15kb
|   |   `-- raw_calls
|   |-- ngmlr_hifi_18kb
|   |   `-- raw_calls
|   |-- winnowmap_hifi_10kb
|   |   `-- raw_calls
|   |-- winnowmap_hifi_15kb
|   |   `-- raw_calls
|   `-- winnowmap_hifi_18kb
|       `-- raw_calls
|-- ONT
|   |-- ExTD_hq_trio_validation
|   |-- lra_ont_19kb
|   |   `-- raw_calls
|   |-- lra_ont_30kb
|   |   `-- raw_calls
|   |-- lra_ont_9kb
|   |   `-- raw_calls
|   |-- minimap2_ont_19kb
|   |   `-- raw_calls
|   |-- minimap2_ont_30kb
|   |   `-- raw_calls
|   |-- minimap2_ont_9kb
|   |   `-- raw_calls
|   |-- ngmlr_ont_19kb
|   |   `-- raw_calls
|   |-- ngmlr_ont_30kb
|   |   `-- raw_calls
|   |-- ngmlr_ont_9kb
|   |   `-- raw_calls
|   |-- winnowmap_ont_19kb
|   |   `-- raw_calls
|   |-- winnowmap_ont_30kb
|   |   `-- raw_calls
|   `-- winnowmap_ont_9kb
|       `-- raw_calls
`-- truvari

truvari directory

.
└── assembly_read_truvari.tsv

aligner_dataset directory

Under subdirectory like minimap2_ont_9kb, you will find:

minimap2_ont_9kb
`-- raw_calls
    |-- HG002.cutesv.s5.vcf
    |-- HG002.pbsv.s5.vcf
    |-- HG002.sniffles.s5.vcf
    |-- HG002.svim.s5.vcf
    |-- HG002.svision.s5.vcf
    |-- pav_HG002.flye.vcf.gz
    |-- pav_HG002.shasta.vcf.gz
    |-- variants.flye.vcf
    `-- variants.shasta.vcf

CMRGs directory

├── assembly_read_cmrgs_truvari.tsv
├── plat_compare
│   ├── assm.HiFi.3sets-fn.merged.vcf
│   ├── assm.HiFi.3sets-fp.merged.vcf
│   ├── assm.HiFi.fn.merged.vcf
│   ├── assm.HiFi.fp.merged.vcf
│   ├── assm.ONT.3sets-fn.merged.vcf
│   ├── assm.ONT.3sets-fp.merged.vcf
│   ├── assm.ONT.fn.merged.vcf
│   ├── assm.ONT.fp.merged.vcf
│   ├── assm.plat.fns.merged.vcf
│   ├── assm_plat_fn.txt
│   ├── assm.plat.fps.merged.vcf
│   ├── assm_plat_fp.txt
│   ├── read.HiFi.3sets-fn.merged.vcf
│   ├── read.HiFi.3sets-fp.merged.vcf
│   ├── read.HiFi.fn.merged.vcf
│   ├── read.HiFi.fp.merged.vcf
│   ├── read.ONT.3sets-fn.merged.vcf
│   ├── read.ONT.3sets-fp.merged.vcf
│   ├── read.ONT.fn.merged.vcf
│   ├── read.ONT.fp.merged.vcf
│   ├── read.plat.fns.merged.vcf
│   ├── read_plat_fn.txt
│   ├── read.plat.fps.merged.vcf
│   └── read_plat_fp.txt
├── stra_compare
│   ├── stra.HiFi.fns.merged.vcf
│   ├── stra.HiFi.fps.merged.vcf
│   ├── stra.ONT.fns.merged.vcf
│   ├── stra.ONT.fps.merged.vcf
│   └── tmp.txt
└── stra_diffcov_truvari.tsv

NOTE: SVIM-asm calls are named as variants.xxx.vcf. Assembly-based calls are only detected from contigs aligned by lra and minimap2, so that they can only be find under directory of prefix lra_xxx and minimap2_xxx

ExTD hq trio validation directory

Files under directory ./ExTD_hq_trio_validation includes:

├── ttmars_combined_res.del.HG003.txt
├── ttmars_combined_res.del.HG004.txt
├── ttmars_combined_res.ins.HG003.txt
├── ttmars_combined_res.ins.HG004.txt
├── ttmars_trio_invalid_insdel.annot.tsv
├── ttmars_trio_invalid_insdel.discpos.tsv
├── ttmars_trio_invalid_insdel.discsize.tsv
├── ttmars_trio_invalid_insdel.inconclu.tsv
├── ttmars_trio_invalid_insdel.nosigs.tsv
├── ttmars_trio_invalid_insdel.tsv
├── vapor_del_HG003.tsv
├── vapor_del_HG004.tsv
├── vapor_ins_HG003.tsv
├── vapor_ins_HG004.tsv
└── vapor_trio_invalid_insdel.tsv