CRAM¶
The cram workflow can be run when starting with already aligned BAM/CRAM files.
Samplesheet¶
family_id proband individual_id hpo_ids sequencing_platform cram sequencing_method regions
fam0 true NA12878 HP:0001626,HP:0000707 illumina illumina_WES_GRCh38_chr20.cram WES single.bed
The required cram file can be downloaded from the test resources folder. The required bed and config files can be downloaded from GitHub.
Run the pipeline¶
vip.sh --workflow cram --input samplesheet.tsv --config single.cfg --output path/to/output/folder
Output files¶
.
├── coverage
│ ├── vip_fam0_NA12878_mosdepth.global.dist.txt
│ ├── vip_fam0_NA12878_mosdepth.per-base.bed.gz
│ ├── vip_fam0_NA12878_mosdepth.per-base.bed.gz.csi
│ ├── vip_fam0_NA12878_mosdepth.region.dist.txt
│ ├── vip_fam0_NA12878_mosdepth.regions.bed.gz
│ ├── vip_fam0_NA12878_mosdepth.regions.bed.gz.csi
│ ├── vip_fam0_NA12878_mosdepth.summary.txt
│ ├── vip_fam0_NA12878_mosdepth.thresholds.bed.gz
│ └── vip_fam0_NA12878_mosdepth.thresholds.bed.gz.csi
├── intermediates
│ ├── NA12878_snv.g.vcf.gz
│ ├── NA12878_snv.g.vcf.gz.csi
│ ├── NA12878_snv.g.vcf.gz.stats
│ ├── vip_annotations.vcf.gz
│ ├── vip_annotations.vcf.gz.csi
│ ├── vip_classifications.vcf.gz
│ ├── vip_classifications.vcf.gz.csi
│ ├── vip_complete_snv.vcf.gz
│ ├── vip_complete_snv.vcf.gz.csi
│ ├── vip_complete_snv.vcf.gz.stats
│ ├── vip_fam0_NA12878_str.vcf.gz
│ ├── vip_fam0_NA12878_str.vcf.gz.csi
│ ├── vip_fam0_NA12878_str.vcf.gz.stats
│ ├── vip_mtdnasnv.vcf.gz
│ ├── vip_mtdnasnv.vcf.gz.csi
│ ├── vip_mtdnasnv.vcf.gz.stats
│ ├── vip_sample_classifications.vcf.gz
│ ├── vip_sample_classifications.vcf.gz.csi
│ ├── vip_snv.vcf.gz
│ ├── vip_snv.vcf.gz.csi
│ ├── vip_snv.vcf.gz.stats
│ ├── vip_sv.vcf.gz
│ ├── vip_sv.vcf.gz.csi
│ ├── vip_sv.vcf.gz.stats
│ ├── vip.vcf.gz
│ ├── vip.vcf.gz.csi
│ └── vip.vcf.gz.stats
├── job.err
├── job.out
├── nxf_report.html
├── nxf_timeline.html
├── samplesheet.tsv
├── vip.db
├── vip.html
├── vip.vcf.gz
└── vip.vcf.gz.csi