File: [panel-id].gatk

  • Updated


[panel-id].gatk is a file with 4 columns – chromosome number, insert start position, insert end position, and amplicon ID. The insert coordinates in this file are used by Tapestri Pipeline in the GATK HaplotypeCaller step to call variants.

It shows one-based, fully closed coordinates for the insert.

View more details about the coordinate system here.

For custom panels with predesigned workflow, the predesigned and newly created amplicon information will be available in the same format as above. The predesigned amplicons will have a different amplicon ID prefix: TAMPL.

Share this article:

Was this article helpful?

0 out of 0 found this helpful

Have more questions? Submit a request