Standard file formats

Submit original format files

The assessment of sample data quality only works on properly formatted files. Most bioinformatics workflows will produce files of the correct format. Use original files for submission. A standard VCF file will fail if it lacks the FORMAT GT or the sample column.

While for example the VCF and BED files can be visualised in text editors or a spreadsheet program such as Excel, editing and saving them from those applications will modify the format, which will make them unacceptable for submission.

The submission system will check the format of the file upon submission. If there is a problem with the file, the system will return an error message to the user. Some typical error cases can be recognised and the error message will let the user know what the problem is. However, in many cases, it will not be possible to identify the error. The user will then be asked to go back to the original files as they came out of the bioinformatics pipeline. If you are struggling to get this to work, we recommend that you contact your EQA provider using the contact information given in the EQA scheme instructions.

VCF file standard

Specifications for the variant calling format VCFv4.1 (link to PDF file with specifications) and VCFv4.2 (link to PDF file with 4.2 specifications) in their most typical encoding can be found on the samtools project page. See also On editing original data files.

BED file standard

The BED format provides a flexible way to define the data lines that are displayed in an annotation track. Please use the same BED file that was used during or after variant calling, to avoid discrepancy in the chromosome naming policy ensuing from the US standard being different. This assessment system accepts only single track BED files. More information about BED file format can be found on the Ensembl pages.