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
orRNA
) and the librar type (e.g.,mRNA_seq
orWES
).
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