# Example output for PacBio WGS Variant Pipeline

## About

These are example output files for the [PacBio WGS Variant Pipeline](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL#pacbio-wgs-variant-pipeline).  Output file types are described in the workflow README.

## Inputs

- HG002/HG003/HG004 trio
- one Revio SMRT Cell per sample
- ~30-fold depth/sample

We used `-rep1` for each sample, and the unaligned BAM files can be downloaded [here](https://downloads.pacbcloud.com/public/revio/2022Q4/).

## Workflow version

pre-v1-release-candidate (functionally identical to v1.0.3)

## Tool versions

- pbmm2 1.10.0
- DeepVariant 1.5.0
- pbsv 2.9.0
- HiPhase 0.10.2
- HiFiCNV 0.1.7
- TRGT 0.5.0
- Paraphase 2.17
- pb-cpg-tools 2.3.2
- GLnexus 1.4.3

## File Listing

```
.
├── README.md
├── alignments
│   ├── HG002.GRCh38.haplotagged.bam
│   ├── HG002.GRCh38.haplotagged.bam.bai
│   ├── HG002.GRCh38.haplotagged.mosdepth.summary.txt
│   ├── HG002.GRCh38.hiphase.blocks.tsv
│   ├── HG002.GRCh38.hiphase.haplotags.tsv
│   ├── HG002.GRCh38.hiphase.stats.tsv
│   ├── HG002.m84011_220902_175841_s1.hifi_reads.read_length_and_quality.tsv
│   ├── HG002.m84011_220902_175841_s1.hifi_reads.read_length_summary.tsv
│   ├── HG002.m84011_220902_175841_s1.hifi_reads.read_quality_summary.tsv
│   ├── HG003.GRCh38.haplotagged.bam
│   ├── HG003.GRCh38.haplotagged.bam.bai
│   ├── HG003.GRCh38.haplotagged.mosdepth.summary.txt
│   ├── HG003.GRCh38.hiphase.blocks.tsv
│   ├── HG003.GRCh38.hiphase.haplotags.tsv
│   ├── HG003.GRCh38.hiphase.stats.tsv
│   ├── HG003.m84010_220919_235306_s2.hifi_reads.read_length_and_quality.tsv
│   ├── HG003.m84010_220919_235306_s2.hifi_reads.read_length_summary.tsv
│   ├── HG003.m84010_220919_235306_s2.hifi_reads.read_quality_summary.tsv
│   ├── HG004.GRCh38.haplotagged.bam
│   ├── HG004.GRCh38.haplotagged.bam.bai
│   ├── HG004.GRCh38.haplotagged.mosdepth.summary.txt
│   ├── HG004.GRCh38.hiphase.blocks.tsv
│   ├── HG004.GRCh38.hiphase.haplotags.tsv
│   ├── HG004.GRCh38.hiphase.stats.tsv
│   ├── HG004.m84010_220919_232145_s1.hifi_reads.read_length_and_quality.tsv
│   ├── HG004.m84010_220919_232145_s1.hifi_reads.read_length_summary.tsv
│   └── HG004.m84010_220919_232145_s1.hifi_reads.read_quality_summary.tsv
├── cohort
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.vcf.gz.tbi
│   ├── HG002_trio_revio.joint.GRCh38.hiphase.blocks.tsv
│   ├── HG002_trio_revio.joint.GRCh38.hiphase.stats.tsv
│   ├── HG002_trio_revio.joint.GRCh38.pbsv.phased.vcf.gz
│   └── HG002_trio_revio.joint.GRCh38.pbsv.phased.vcf.gz.tbi
├── cpg
│   ├── HG002.GRCh38.combined.bed
│   ├── HG002.GRCh38.combined.bw
│   ├── HG002.GRCh38.hap1.bed
│   ├── HG002.GRCh38.hap1.bw
│   ├── HG002.GRCh38.hap2.bed
│   ├── HG002.GRCh38.hap2.bw
│   ├── HG003.GRCh38.combined.bed
│   ├── HG003.GRCh38.combined.bw
│   ├── HG003.GRCh38.hap1.bed
│   ├── HG003.GRCh38.hap1.bw
│   ├── HG003.GRCh38.hap2.bed
│   ├── HG003.GRCh38.hap2.bw
│   ├── HG004.GRCh38.combined.bed
│   ├── HG004.GRCh38.combined.bw
│   ├── HG004.GRCh38.hap1.bed
│   ├── HG004.GRCh38.hap1.bw
│   ├── HG004.GRCh38.hap2.bed
│   └── HG004.GRCh38.hap2.bw
├── deepvariant
│   ├── HG002.GRCh38.deepvariant.g.vcf.gz
│   ├── HG002.GRCh38.deepvariant.g.vcf.gz.tbi
│   ├── HG002.GRCh38.deepvariant.phased.vcf.gz
│   ├── HG002.GRCh38.deepvariant.phased.vcf.gz.tbi
│   ├── HG002.GRCh38.deepvariant.roh.bed
│   ├── HG002.GRCh38.deepvariant.vcf.stats.txt
│   ├── HG003.GRCh38.deepvariant.g.vcf.gz
│   ├── HG003.GRCh38.deepvariant.g.vcf.gz.tbi
│   ├── HG003.GRCh38.deepvariant.phased.vcf.gz
│   ├── HG003.GRCh38.deepvariant.phased.vcf.gz.tbi
│   ├── HG003.GRCh38.deepvariant.roh.bed
│   ├── HG003.GRCh38.deepvariant.vcf.stats.txt
│   ├── HG004.GRCh38.deepvariant.g.vcf.gz
│   ├── HG004.GRCh38.deepvariant.g.vcf.gz.tbi
│   ├── HG004.GRCh38.deepvariant.phased.vcf.gz
│   ├── HG004.GRCh38.deepvariant.phased.vcf.gz.tbi
│   ├── HG004.GRCh38.deepvariant.roh.bed
│   └── HG004.GRCh38.deepvariant.vcf.stats.txt
├── hificnv
│   ├── hificnv.HG002.copynum.bedgraph
│   ├── hificnv.HG002.depth.bw
│   ├── hificnv.HG002.maf.bw
│   ├── hificnv.HG002.vcf.gz
│   ├── hificnv.HG002.vcf.gz.tbi
│   ├── hificnv.HG003.copynum.bedgraph
│   ├── hificnv.HG003.depth.bw
│   ├── hificnv.HG003.maf.bw
│   ├── hificnv.HG003.vcf.gz
│   ├── hificnv.HG003.vcf.gz.tbi
│   ├── hificnv.HG004.copynum.bedgraph
│   ├── hificnv.HG004.depth.bw
│   ├── hificnv.HG004.maf.bw
│   ├── hificnv.HG004.vcf.gz
│   └── hificnv.HG004.vcf.gz.tbi
├── paraphase
│   ├── HG002.json
│   ├── HG002_cfc1_hap1.vcf
│   ├── HG002_cfc1_hap2.vcf
│   ├── HG002_cfc1_hap3.vcf
│   ├── HG002_cfc1_variants.vcf
│   ├── HG002_ncf1_ncf1_hap1.vcf
│   ├── HG002_ncf1_ncf1_hap2.vcf
│   ├── HG002_ncf1_pseudo_hap1.vcf
│   ├── HG002_ncf1_pseudo_hap2.vcf
│   ├── HG002_ncf1_pseudo_hap3.vcf
│   ├── HG002_ncf1_variants.vcf
│   ├── HG002_neb_hap1.vcf
│   ├── HG002_neb_hap2.vcf
│   ├── HG002_neb_hap3.vcf
│   ├── HG002_neb_hap4.vcf
│   ├── HG002_neb_hap5.vcf
│   ├── HG002_neb_hap6.vcf
│   ├── HG002_neb_variants.vcf
│   ├── HG002_pms2_pms2clhap1.vcf
│   ├── HG002_pms2_pms2clhap2.vcf
│   ├── HG002_pms2_pms2hap1.vcf
│   ├── HG002_pms2_pms2hap2.vcf
│   ├── HG002_pms2_variants.vcf
│   ├── HG002_rccx_hap1.vcf
│   ├── HG002_rccx_hap2.vcf
│   ├── HG002_rccx_hap3.vcf
│   ├── HG002_rccx_hap4.vcf
│   ├── HG002_rccx_variants.vcf
│   ├── HG002_realigned_tagged.bam
│   ├── HG002_realigned_tagged.bam.bai
│   ├── HG002_smn1_smn1hap1.vcf
│   ├── HG002_smn1_smn1hap2.vcf
│   ├── HG002_smn1_smn2hap1.vcf
│   ├── HG002_smn1_smn2hap2.vcf
│   ├── HG002_smn1_variants.vcf
│   ├── HG002_strc_strc_hap1.vcf
│   ├── HG002_strc_strc_hap2.vcf
│   ├── HG002_strc_strcp1_hap1.vcf
│   ├── HG002_strc_strcp1_hap2.vcf
│   ├── HG002_strc_variants.vcf
│   ├── HG003.json
│   ├── HG003_cfc1_hap1.vcf
│   ├── HG003_cfc1_hap2.vcf
│   ├── HG003_cfc1_hap3.vcf
│   ├── HG003_cfc1_hap4.vcf
│   ├── HG003_cfc1_variants.vcf
│   ├── HG003_ikbkg_ikbkg_hap1.vcf
│   ├── HG003_ikbkg_pseudo_hap1.vcf
│   ├── HG003_ikbkg_variants.vcf
│   ├── HG003_ncf1_ncf1_hap1.vcf
│   ├── HG003_ncf1_ncf1_hap2.vcf
│   ├── HG003_ncf1_pseudo_hap1.vcf
│   ├── HG003_ncf1_pseudo_hap2.vcf
│   ├── HG003_ncf1_pseudo_hap3.vcf
│   ├── HG003_ncf1_variants.vcf
│   ├── HG003_neb_hap1.vcf
│   ├── HG003_neb_hap2.vcf
│   ├── HG003_neb_hap3.vcf
│   ├── HG003_neb_hap4.vcf
│   ├── HG003_neb_hap5.vcf
│   ├── HG003_neb_hap6.vcf
│   ├── HG003_neb_variants.vcf
│   ├── HG003_pms2_pms2clhap1.vcf
│   ├── HG003_pms2_pms2clhap2.vcf
│   ├── HG003_pms2_pms2hap1.vcf
│   ├── HG003_pms2_pms2hap2.vcf
│   ├── HG003_pms2_variants.vcf
│   ├── HG003_rccx_hap1.vcf
│   ├── HG003_rccx_hap2.vcf
│   ├── HG003_rccx_hap3.vcf
│   ├── HG003_rccx_hap4.vcf
│   ├── HG003_rccx_variants.vcf
│   ├── HG003_realigned_tagged.bam
│   ├── HG003_realigned_tagged.bam.bai
│   ├── HG003_smn1_smn1hap1.vcf
│   ├── HG003_smn1_smn1hap2.vcf
│   ├── HG003_smn1_smn2hap1.vcf
│   ├── HG003_smn1_smn2hap2.vcf
│   ├── HG003_smn1_variants.vcf
│   ├── HG003_strc_strc_hap1.vcf
│   ├── HG003_strc_strc_hap2.vcf
│   ├── HG003_strc_strcp1_hap1.vcf
│   ├── HG003_strc_strcp1_hap2.vcf
│   ├── HG003_strc_variants.vcf
│   ├── HG004.json
│   ├── HG004_cfc1_hap1.vcf
│   ├── HG004_cfc1_hap2.vcf
│   ├── HG004_cfc1_hap3.vcf
│   ├── HG004_cfc1_variants.vcf
│   ├── HG004_ikbkg_ikbkg_hap1.vcf
│   ├── HG004_ikbkg_ikbkg_hap2.vcf
│   ├── HG004_ikbkg_pseudo_hap1.vcf
│   ├── HG004_ikbkg_pseudo_hap2.vcf
│   ├── HG004_ikbkg_variants.vcf
│   ├── HG004_ncf1_ncf1_hap1.vcf
│   ├── HG004_ncf1_ncf1_hap2.vcf
│   ├── HG004_ncf1_pseudo_hap1.vcf
│   ├── HG004_ncf1_pseudo_hap2.vcf
│   ├── HG004_ncf1_pseudo_hap3.vcf
│   ├── HG004_ncf1_pseudo_hap4.vcf
│   ├── HG004_ncf1_variants.vcf
│   ├── HG004_neb_hap1.vcf
│   ├── HG004_neb_hap2.vcf
│   ├── HG004_neb_hap3.vcf
│   ├── HG004_neb_hap4.vcf
│   ├── HG004_neb_hap5.vcf
│   ├── HG004_neb_variants.vcf
│   ├── HG004_pms2_pms2clhap1.vcf
│   ├── HG004_pms2_pms2clhap2.vcf
│   ├── HG004_pms2_pms2hap1.vcf
│   ├── HG004_pms2_variants.vcf
│   ├── HG004_rccx_hap1.vcf
│   ├── HG004_rccx_hap2.vcf
│   ├── HG004_rccx_hap3.vcf
│   ├── HG004_rccx_hap4.vcf
│   ├── HG004_rccx_variants.vcf
│   ├── HG004_realigned_tagged.bam
│   ├── HG004_realigned_tagged.bam.bai
│   ├── HG004_smn1_smn1hap1.vcf
│   ├── HG004_smn1_smn1hap2.vcf
│   ├── HG004_smn1_smn2hap1.vcf
│   ├── HG004_smn1_smn2hap2.vcf
│   ├── HG004_smn1_variants.vcf
│   ├── HG004_strc_strc_hap1.vcf
│   ├── HG004_strc_strc_hap2.vcf
│   ├── HG004_strc_strcp1_hap1.vcf
│   ├── HG004_strc_strcp1_hap2.vcf
│   └── HG004_strc_variants.vcf
├── pbsv
│   ├── HG002.GRCh38.pbsv.phased.vcf.gz
│   ├── HG002.GRCh38.pbsv.phased.vcf.gz.tbi
│   ├── HG003.GRCh38.pbsv.phased.vcf.gz
│   ├── HG003.GRCh38.pbsv.phased.vcf.gz.tbi
│   ├── HG004.GRCh38.pbsv.phased.vcf.gz
│   └── HG004.GRCh38.pbsv.phased.vcf.gz.tbi
├── tertiary
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.compound_hets.tsv
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.compound_hets.vcf.gz
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.compound_hets.vcf.gz.tbi
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.tsv
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.vcf.gz
│   ├── HG002_trio_revio.joint.GRCh38.deepvariant.glnexus.phased.norm.slivar.vcf.gz.tbi
│   ├── HG002_trio_revio.joint.GRCh38.pbsv.phased.svpack.tsv
│   ├── HG002_trio_revio.joint.GRCh38.pbsv.phased.svpack.vcf.gz
│   └── HG002_trio_revio.joint.GRCh38.pbsv.phased.svpack.vcf.gz.tbi
└── trgt
    ├── HG002.GRCh38.haplotagged.trgt.sorted.vcf.gz
    ├── HG002.GRCh38.haplotagged.trgt.sorted.vcf.gz.tbi
    ├── HG002.GRCh38.haplotagged.trgt.spanning.sorted.bam
    ├── HG002.GRCh38.haplotagged.trgt.spanning.sorted.bam.bai
    ├── HG002.GRCh38.trgt.dropouts.txt
    ├── HG003.GRCh38.haplotagged.trgt.sorted.vcf.gz
    ├── HG003.GRCh38.haplotagged.trgt.sorted.vcf.gz.tbi
    ├── HG003.GRCh38.haplotagged.trgt.spanning.sorted.bam
    ├── HG003.GRCh38.haplotagged.trgt.spanning.sorted.bam.bai
    ├── HG003.GRCh38.trgt.dropouts.txt
    ├── HG004.GRCh38.haplotagged.trgt.sorted.vcf.gz
    ├── HG004.GRCh38.haplotagged.trgt.sorted.vcf.gz.tbi
    ├── HG004.GRCh38.haplotagged.trgt.spanning.sorted.bam
    ├── HG004.GRCh38.haplotagged.trgt.spanning.sorted.bam.bai
    └── HG004.GRCh38.trgt.dropouts.txt

9 directories, 243 files
```