Generic Sample Sheets

We describe call using a sample sheet not following the matched cancer or germline variants schema generic sample sheets. These can be used to describe arbitrary biomedical experiments. There is no restriction on the structure of such a sample sheet.

However, there also is a shortcut TSV format to describe such sample sheets that has some restrictions.

Generic TSV Schema

The following assumptions must hold when using the generic TSV schema:

  • Each bio entity must have at least one bio sample, each bio sample at least one test sample, and each test sample at least one NGS library.
  • You have to explicitely assign a secondary ID to each object in this tree.
  • The files of each NGS library are below the same folder.
  • You have to define the extraction type (e.g., DNA or RNA) and the librar type (e.g., mRNA_seq or WES).

A minimal generic TSV file (with header) looks as follows:

[Metadata]
schema	generic_experiment
schema_version	v1
title	Example generic experiment
description	This is an example for a generic experiment.

[Data]
bioEntity	bioSample	testSample	ngsLibrary	extractionType	libraryType	folderName
E001	BS1	TS1	LIB1	RNA	total_RNA_seq	E001-BS1-TS1-LIB1
E001	BS2	TS1	LIB1	RNA	total_RNA_seq	E001-BS2-TS1-LIB1
E002	BS1	TS1	LIB1	RNA	total_RNA_seq	E002-BS1-TS1-LIB1
E002	BS1	TS1	LIB2	RNA	total_RNA_seq	E001-BS1-TS1-LIB2

Again, the header can be omitted, then the file starts after the [Data] line. All further information has to be described using custom fields as described in the section Custom Fields in TSV Schemas. For example with additional information:

[Metadata]
schema	generic_experiment
schema_version	v1
title	Example generic experiment
description	This is an example for a generic experiment.

[Custom Fields]
key	annotatedEntity	docs	type	minimum	maximum	unit	choices	pattern
cellLine	bioEntity	Cell line name	enum	.	.	.	HELA,HEK	.
treatment	bioEntity	Cell line treatment	enum	.	.	.	Ibrutinib,Nivolumap,control	.
replicate	bioEntity	Replicate identifier	string	.	.	.	.	.

[Data]
bioEntity	bioSample	testSample	ngsLibrary	extractionType	libraryType	folderName	cellLine	treatment	replicate
HELA_control_A	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_control_A-BS1-TS1-LIB1	HELA	control	A
HELA_control_C	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_control_C-BS1-TS1-LIB1	HELA	control	C
HELA_Ibrutinib_A	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_Ibrutinib_A-BS1-TS1-LIB1	HELA	Ibrutinib	A
HELA_Ibrutinib_B	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_Ibrutinib_B-BS1-TS1-LIB1	HELA	Ibrutinib	B
HELA_Nivolumap_A	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_Nivolumap_A-BS1-TS1-LIB1	HELA	Nivolumap	A
HELA_Nivolumap_B	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_Nivolumap_B-BS1-TS1-LIB1	HELA	Nivolumap	B
HELA_Nivolumap_C	BS1	TS1	LIB1	RNA	mRNA_seq	HELA_Nivolumap_C-BS1-TS1-LIB1	HELA	Nivolumap	C
HEK_control_A	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_control_A-BS1-TS1-LIB1	HEK	control	A
HEK_control_B	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_control_B-BS1-TS1-LIB1	HEK	control	B
HEK_control_C	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_control_C-BS1-TS1-LIB1	HEK	control	C
HEK_Ibrutinib_A	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_Ibrutinib_A-BS1-TS1-LIB1	HEK	Ibrutinib	A
HEK_Ibrutinib_B	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_Ibrutinib_B-BS1-TS1-LIB1	HEK	Ibrutinib	B
HEK_Nivolumap_B	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_Nivolumap_B-BS1-TS1-LIB1	HEK	Nivolumap	B
HEK_Nivolumap_C	BS1	TS1	LIB1	RNA	mRNA_seq	HEK_Nivolumap_C-BS1-TS1-LIB1	HEK	Nivolumap	C