How to create a samplesheet

A samplesheet describes the structure of your input genotyping datasets. It's needed because the structure of input data can be very different across use cases (e.g. different file formats, directories, and split vs. unsplit by chromosome).

tip

Samplesheets can be in CSV, TSV, JSON, or YAML format

Warnings before you get started

Preparing your target genomes

• pgsc_calc works best with cohort data
• Scores calculated for low sample sizes will generate warnings in the output report
• You should merge your genomes if they are split per individual before using pgsc_calc

Chromosomes

• In the initial release only autosomes are supported (1-22)
• X, Y, and MT support will be added in the next release

Imputation and WGS support

• Array data should be imputed (e.g. TopMed/Michigan) to increase variant density
• If you use unimputed array data then many scores will probably fail to calculate
• wgs support will be added in v3-rc2

Sample batches aren't supported yet, and low sample sizes aren't great

• A target genome must contain every sample in a single file
• For example, this means that splitting VCFs into batches of 100,000 samples is not supported (chrom1_batch1, chrom1_batch2, ...)
• This limitation will be removed in a future release candidate

Samplesheet structure

Column name	Mandatory	Description
sampleset	✅	A text string (no spaces) referring to the name of a target dataset of genotyping data containing at least one sample/individual. Data from a sampleset may be input as a single file, or split across chromosomes into multiple files.
path	✅	Should be set to the path of the target genome file. Absolute paths are best.
chrom	✅	An integer (range 1-22) or string (X, Y). If the target genomic data file contains multiple chromosomes, leave empty. Don't use a mix of empty and integer chromosomes in the same sampleset.
file_format	✅	The file format of the target genomes. Currently supports bgen and vcf.
genotyping_method	✅	How were genotypes called? array or wgs
bgen_sample_file	❌	Path to the BGEN sample file, which contains sample identifiers. Mandatory if format is bgen.

Simple samplesheet example

What's a simple samplesheet?

This example assumes your VCF/BGEN file contains multiple chromosomes and multiple samples.

A samplesheet can be set up in a spreadsheet program, using the following structure:

sampleset	path	chrom	file_format	genotyping_method	bgen_sample_file
1000G	tests/data/bgen/PGS000586_GRCh38.bgen		bgen	array	tests/data/bgen/PGS000586_GRCh38.sample

Complex samplesheet example

What's a complex samplesheet?

• This example assumes each VCF/BGEN file contains one chromosome and multiple samples
• Each row corresponds to a different chromosome in the same sampleset

sampleset	path	chrom	file_format	genotyping_method
1000G	tests/data/vcf/split/PGS000586_GRCh38_1.vcf.gz	1	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_2.vcf.gz	2	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_3.vcf.gz	3	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_4.vcf.gz	4	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_5.vcf.gz	5	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_6.vcf.gz	6	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_7.vcf.gz	7	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_8.vcf.gz	8	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_9.vcf.gz	9	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_10.vcf.gz	10	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_11.vcf.gz	11	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_12.vcf.gz	12	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_13.vcf.gz	13	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_14.vcf.gz	14	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_15.vcf.gz	15	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_16.vcf.gz	16	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_17.vcf.gz	17	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_18.vcf.gz	18	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_19.vcf.gz	19	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_20.vcf.gz	20	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_21.vcf.gz	21	vcf	array
1000G	tests/data/vcf/split/PGS000586_GRCh38_22.vcf.gz	22	vcf	array