Sample Management
Samples are central to every analysis. For every query, a sample needs to be submitted which is used to filter the variants. All SNV's are associated with one or more sample. A family is denoted by a pedigree id. Filling out sample and pedigree information is prerequisite to the other data upload scripts and can be achieved using a pre-formatted sample sheet.
Sample Management
To add new samples to the system, please follow the following procedure:
- Create a sample sheet (Example)
- Upload the sample sheet through "Import External Data"
- Add family information for each sample
Sample Sheets
A sample sheet can be created as a basic comma separated file. The following columns are mandatory.
Column | Description |
---|---|
Sample ID | Unique sample identifier |
Foreign ID | Secondary sample identifier (f.e. external IDs) |
Pedigree | Family id denoting members of one family |
Comment | Arbitrary comment |
Sex | Sex of the patient ("male" or "female") |
Affected | Affectedness (0/1) |
Organism | Sequenced organism |
Tissue | Tissue that was sequenced (peripheral blood etc.) |
Disease | A name of a disease (must exist in the database) |
Library Type | Sequencing library type |
Read Type | Library sequencing protocol type |
Exome Assay | Exome capture kit used for sequencing |
Example Sample Sheet
Table
Sample ID | Foreign ID | Pedigree | Comment | Sex | Affected | Organism | Tissue | Disease | Library Type | Read Type | Exome Assay |
---|---|---|---|---|---|---|---|---|---|---|---|
76436 | 76436 | B20-0498 | TranslateNamse | female | 1 | human | peripheral blood | Cases | exomic | paired-end | SureSelect60Mbv6 |
76443 | 76443 | B20-0498 | TranslateNamse | male | 0 | human | peripheral blood | Controls | exomic | paired-end | SureSelect60Mbv6 |
76442 | 76442 | B20-0498 | TranslateNamse | female | 0 | human | peripheral blood | Controls | exomic | paired-end | SureSelect60Mbv6 |
.csv File
Sample ID,Foreign ID,Pedigree,Comment,Sex,Affected,Organism,Tissue,Disease,Library Type,Read Type,Exome Assay
76436,76436,B20-0498,TranslateNamse,female,1,human,peripheral blood,Cases,exomic,paired-end,SureSelect60Mbv6
76443,76443,B20-0498,TranslateNamse,male,0,human,peripheral blood,Controls,exomic,paired-end,SureSelect60Mbv6
76442,76442,B20-0498,TranslateNamse,female,0,human,peripheral blood,Controls,exomic,paired-end,SureSelect60Mbv6
Import External Sample
Once you created your sample sheet, it should be uploaded by using the
Import external samples
form within the admin application.
Missing Features
Some parts of the import external samples form refer to features that are
currently unavailable within the docker or other external deployments. Make
sure to set File Extensions
to no files
, otherwise the import will
fail.
Entering Family Information
While the pedigree ID for each sample can be specified in the sample sheet, the precise family structure can not. For this it is necessary to go through the manual process using the UI. To add family information to a sample, you have to use the admin application.
In the admin application, use the following procedure to add the pedigree information (i.e. father/mother).
- Find the sample using
Search samples
- Click on the
Id
column of the sample you want to modify - Enter
mother
andfather
in the corresponding rows