When generating the QC.html, we think the table in section 4.2 "Reconfirming genetic relationships are correct" is identifying the samples which have been filtered out during QC as samples from the same individual. The genetically identical samples are correctly identified in section 3.1 but an additional column appears postQC in section 4.2 and corresponds to the number of samples that have been removed during QC in my dataset.
How can the bug be reproduced?
The data I am using to generate the QC.html is not currently publicly available. However, please just let me know if I can provide any further information.
Contact Details
me460@exeter.ac.uk
What happened?
When generating the QC.html, we think the table in section 4.2 "Reconfirming genetic relationships are correct" is identifying the samples which have been filtered out during QC as samples from the same individual. The genetically identical samples are correctly identified in section 3.1 but an additional column appears postQC in section 4.2 and corresponds to the number of samples that have been removed during QC in my dataset.
How can the bug be reproduced?
The data I am using to generate the QC.html is not currently publicly available. However, please just let me know if I can provide any further information.
Relevant log output
No response