Progenetix data is licenced under CC-BY 4.0 and can be freely downloaded for research and commercial purposes, with the stipulation of proper acknowledgement.
The data is provided eiher as JSON or tab-delimited text files, depending on the type of data. For several purposes both options are available.
Inseveral places throughout the sample and subset pages one can find links for the download of e.g. data returned from sample searches. The example above shows the standard link for the CNV frequency file corresponding to the histogram data.
The Progenetix resource utilizes the Beacon v2 API for data delivery. Some information about the standard paths & their usage can be found on the Beacon v2 path examples page. Below are the examples for the main direct data access scenarios.
The different filter options are described on the Filter Documentation page.
&method=callsetsvariantsfor any download of more-than-a-few samples; this will start to stream the variants instead of pre-fetching them (which may time out the server)
Especially for biosamples it may make sense just to get the data in a tabular
format using the
For use cases where one e.g. just needs the identifiers of a given object, e.g.
to intersect the query results with a previously accessed master table, the
output=idtable format can be used.
The Progenetix API implements a number of “services” which can e.g. be utilized to download aggregate data such as CNV frequency data of a disease entity.
With the maturation of the Beacon v2 protocol and associated data schemas,
the default delivery of JSON encoded data follows the standard Beacon response
format where the main data is contained in the
For more information see the beaconresponse json documentation.
.pgxseg files are tab-delimited, columnar text files where each line provides
information about features or measurements associated with a genomic region.
More information can be found on the file formats page.
.pgxmatrix files are tab-delimited, columnar data matrix files where each line
provides interval-mapped values, usually e.g. for 1Mb genomic intervals of a
sample or classification. More information can be found on the file formats page.