Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"

The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".

Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:

hiphase_vcfs

├── all_vcfs.md5

├── hiphase

│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz

│   ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi

│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz

│   ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi

│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz

│   ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz

│   ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz

│   ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz

│   ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz

│   ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz

│   ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz

│   └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi

├── unphased

│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz

│   ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi

│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz

│   ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi

│   ├── HG002-rep1.GRCh38.trgt.vcf.gz

│   ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz

│   ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz

│   ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi

│   ├── HG002-rep2.GRCh38.trgt.vcf.gz

│   ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz

│   ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz

│   ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi

│   ├── HG002-rep3.GRCh38.trgt.vcf.gz

│   └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi

└── whatshap

    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz

    ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi

    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz

    ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi

    ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz

    └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi

3 directories, 43 files