Input

The --input value is a tab-separated file (sample-sheet) with each row describing the data and metadata of a sample.

A minimal sample-sheet for the vcf workflow could look like this:

individual_id vcf
sample0 sample0.vcf.gz
sample1 sample1.vcf.gz
sample2 sample2.vcf.gz

Sample-sheet values are case sensitive. Columns can contain values of different types:

type description
boolean allowed values: [true, false]
enum categorical value
file absolute file path or file path relative to the sample sheet
file list comma-separated list of file paths
string text
string list comma-separated list of strings

The following sections describe the columns that can be used in every sample-sheet followed by workflow specific columns.

Columns

column type required default description
project_id string vip project identifier, see here
family_id string fam<index> family identifier
individual_id string yes sample identifier of the individual
paternal_id string sample identifier of the father
maternal_id string sample identifier of the mother
sex enum unknown sex values: [male,female] Please note that an unknown sex leads to a Spectre CNV analysis that assumes female for the ploidy determination of chromosome X.
affected boolean unknown affected status whether the individual is affected
proband boolean depends1 individual being reported on
hpo_ids string list regex: /HP:\d{7}/ from HPO v2024-08-13. term must be a child of 'Phenotypic abnormality' (HP:0000118)
sequencing_method enum WGS allowed values: [WES,WGS], value must be the same for all project samples
regions file allowed file extensions: [bed]. filter variants overlapping with regions in bed file2

1 Exception: if no probands are defined in the sample-sheet then all samples are considered to be probands.

Columns: FASTQ

column type required default description
adaptive_sampling file allowed file extensions: [csv]. for nanopore adaptive sampling experiments, used to filter stop_receiving reads
fastq file list yes3 allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. single-reads file(s)
fastq_r1 file list yes3 allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. paired-end reads file(s) #1
fastq_r2 file list yes3 allowed file extensions: [fastq, fastq.gz, fq, fq.gz]. paired-end reads file(s) #2
sequencing_platform enum nanopore allowed values: [illumina,nanopore,pacbio_hifi], value must be the same for all project samples

3 Either the fastq or the fastq_r1 and fastq_r2 are required.

Columns: CRAM

column type required default description
cram file yes allowed file extensions: [bam, cram, sam]
sequencing_platform enum illumina allowed values: [illumina,nanopore,pacbio_hifi], value must be the same for all project samples

Columns: gVCF

column type required default description
assembly enum GRCh38 allowed values: [GRCh37, GRCh38, T2T]
gvcf file yes allowed file extensions: [gvcf, gvcf.gz, gvcf.bgz, vcf, vcf.gz, vcf.bgz, bcf, bcf.gz, bcf.bgz]
cram file allowed file extensions: [bam, cram, sam]

Columns: VCF

column type required default description
assembly enum GRCh38 allowed values: [GRCh37, GRCh38, T2T], value must be the same for all project samples
vcf file yes allowed file extensions: [vcf, vcf.gz, vcf.bgz, bcf, bcf.gz, bcf.bgz], value must be the same for all project samples
cram file allowed file extensions: [bam, cram, sam]