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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:

  1. Create a sample sheet (Example)
  2. Upload the sample sheet through "Import External Data"
  3. 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.

Upload External Sample

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).

  1. Find the sample using Search samples Search Sample Form
  2. Click on the Id column of the sample you want to modify Sample Search Table
  3. Enter mother and father in the corresponding rows Edit Sample Form