Discordant expected dup removal - only apply to replicates pass call rate & contamination

[1teaspoon]

In the example below, since SB745670_PB84781_F05 is below call rate filter, sample SB745670_PB84781_G01 should be kept for subject level analysis. Unless they are both pass call rate & contamination filter, both replicates should be removed.

[jaamarks]

update

We are still experiencing an issue with the retention of expected replicates when one of the samples fails the call rate filters. Specifically, if we have two samples that are expected replicates and one does not pass the call rate filter, the other sample that does pass should still be retained and proceed to subject-level qc.

This did not happen in the case below though. We would expect to retain SB745670_PB84781_G01 since its counterpart SB745670_PB84781_F05 had a low call rate.

Sample_ID	Group_By_Subject_ID	Project	Case/Control_Status	Internal Control	Number Samples Per Subject	Replicate IDs	Sample Excluded from QC	Sample Used in Subject Analysis	Subject Removed	Sample Pass QC	Low Call Rate
SB745670_PB84781_G01	I-0000618499	GP0385-CI21	Control	FALSE	2	SB745670_PB84781_F05|SB745670_PB84781_G01	FALSE	FALSE	TRUE	FALSE	FALSE
SB745670_PB84781_F05	I-0000618499	GP0385-CI21	Control	FALSE	2	SB745670_PB84781_F05|SB745670_PB84781_G01	FALSE	FALSE	TRUE	FALSE	TRUE