gVCF¶

The gvcf workflow can be run when starting with gvcf files.

Samplesheet¶

family_id   individual_id   paternal_id maternal_id sex affected    proband gvcf    cram
FAM0    HG002   HG003   HG004   male    true    true    HG002.illumina.wes.chr20.g.vcf.gz   illumina_WES_GRCh38_chr20.cram
FAM0    HG003           male    false       HG003.illumina.wes.chr20.g.vcf.gz   illumina_WES_GRCh38_chr20.cram
FAM0    HG004           female  false       HG004.illumina.wes.chr20.g.vcf.gz   illumina_WES_GRCh38_chr20.cram

The required cram and gvcf files can be downloaded from the test resources folder.

Run the pipeline¶

vip.sh --workflow gvcf --input samplesheet.tsv --output path/to/output/folder

Output files¶

.
├── intermediates
│   ├── vip_annotations.vcf.gz
│   ├── vip_annotations.vcf.gz.csi
│   ├── vip_classifications.vcf.gz
│   ├── vip_classifications.vcf.gz.csi
│   ├── vip.db
│   ├── vip_sample_classifications.vcf.gz
│   ├── vip_sample_classifications.vcf.gz.csi
│   ├── vip.vcf.gz
│   └── vip.vcf.gz.csi
├── log
│   ├── nxf.log
│   ├── nxf_report.html
│   ├── nxf_timeline.html
│   ├── slurm_job.err
│   └── slurm_job.out
├── samplesheet.tsv
├── tmp
│   ├── nextflow
│   ├── nxf.temp
│   └── nxf.work
├── vip.html
├── vip.vcf.gz
└── vip.vcf.gz.csi