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Idea #11673

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Extend CGF to include genotyping

Added by Abram Connelly almost 7 years ago. Updated almost 5 years ago.

Status:
New
Priority:
Normal
Assigned To:
-
Target version:
Start date:
05/11/2017
Due date:
Story points:
1.0

Description

Extend the CGFv3 format to include genotyping information, not just whole genome information.

We should be able to convert both 23andMe and Ancestry.com data a tiling/CGF representation.

The specification should be updated and the cgft tool should be updated to be able to take in the new band information, store it as CGF and convert back to band information.

The main difference in storage at the CGF layer is that the "low quality" data will be reversed, representing position and length data of high quality data instead of low quality data.
A flag needs to be set in the header in order to differentiate between the two storage interpretations.
Further, since the genotyping data is so small, we can "stuff" in the original data into a data field in the CGF so that we can recreate, up to a reasonable approximation, the original genotyping information.

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