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Submitted by Sheeba on
 

 

Version 1

This pipeline tests each WGS sample, independently. If a sample fails this test, then it is excluded from the aggregation and not released or reported in this document. These tests detect sample swaps, cross-individual contamination, and sample preparation/sequencing errors. The list of specific QC processes is listed in the table below:

QC procedure

Criteria

Sequencing metrics

for sample sequenced before Oct 2023:

Autosomal mean depth of coverage >= 15 X 

for samples sequenced after Oct 2023:

  • ≥ 30x mean coverage 
  • ≥ 90% of bases at 15x coverage 
  • Duplicate rate : < 20%

Median insert size : >= 250

 

 

 

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