Multi-project¶

VIP can be used to analyse different projects in one run, producing output files per project. To achieve this you just need to specify different projects in one samplesheet.

family_id  individual_id    paternal_id maternal_id sex affected    proband sequencing_platform fastq       fastq_r1        fastq_r2
vip0    fam0    individual0 individual1         male    true    true    nanopore        path/to/vip0.fastq.gz
vip0    fam0    individual1                 female  false   false   nanopore        path/to/vip1.fastq.gz
vip1    fam1    individual2 individual3     individual4 male    false   false   paacbio_hifi        path/to/vip2.fastq.gz
vip1    fam1    individual3                 male    false   false   pacbio_hifi     path/to/vip3.fastq.gz
vip1    fam1    individual4                 female  false   true    pacbio_hifi     path/to/vip4.fastq.gz
vip2    fam2    individual5                 male    true    true    illumina                /vip5_1.fastq.gz    /vip5_2.fastq.gz

Run the pipeline¶

cd vip
vip --workflow fastq --input path/to/samplesheet.tsv --output path/to/output/folder

For a working example on how to generate output for multiple projects see here.