SEQNEXT Settings

Please note before download:

  • On this website JSI medical systems provides pre-definied settings for an easy import in our SEQUENCE PILOT module SEQNEXT.
  • The files contain thresholds for variant calling, coverage warning and quality.
  • These settings are only a proposal.
  • The settings might to be adapted depending on your data and needs.
  • The files can be imported only into SEQUENCE PILOT versions 4.4 and higher.

Download

Settings with genome mapping (the raw data are mapped against the complete genome to filter background):

GENOME
TYPE OF VARIANT
DETECTION LIMIT FOR VARIANTS
DOWNLOAD
GENOME
Germline 5 GM
TYPE OF VARIANT
germline
DETECTION LIMIT FOR VARIANTS
5 % / 15 %
GENOME
Germline 10 GM
TYPE OF VARIANT
germline
DETECTION LIMIT FOR VARIANTS
10 % / 20 %
GENOME
Somatic 0.1 GM
TYPE OF VARIANT
somatic
DETECTION LIMIT FOR VARIANTS
0.1 % / 2 %
GENOME
Somatic 1 GM
TYPE OF VARIANT
somatic
DETECTION LIMIT FOR VARIANTS
1 % / 5 %

Settings without genome mapping:

NAME
TYPE OF VARIANTS
DETECTION LIMIT FOR VARIANTS
DOWNLOAD
NAME
Germline 5
TYPE OF VARIANTS
germline
DETECTION LIMIT FOR VARIANTS
5 % / 15 %
NAME
Germline 10
TYPE OF VARIANTS
germline
DETECTION LIMIT FOR VARIANTS
10 % / 20 %
NAME
Somatic 0.1
TYPE OF VARIANTS
somatic
DETECTION LIMIT FOR VARIANTS
0.1 % / 2 %
NAME
Somatic 1
TYPE OF VARIANTS
somatic
DETECTION LIMIT FOR VARIANTS
1 % / 5 %

Installation

  • log into your SEQUENCE PILOT installation
  • go to category SEQNEXT
  • go to operation [Run]
  • press button [Settings]
  • press button [Import...] in the Settings dialogue and select the downloaded see-file
  • press button [OK] in all following dialogues to finish the import