A fix was recently implemented in iVar v. 1.3.1 that addresses an issue with trimming that was identified for some amplicon-based sequencing protocols (e.g. SWIFT, SNAP), where polymerases can add additional bases and lead mismatches.
Prior to this change, the Dockerfile was updated to include this latest version of iVar (https://github.com/chanzuckerberg/idseq-workflows/pull/84). This PR updates the ivar trim call in the TrimPrimers step to leverage the recent change. In particular, it makes the ivar trim command dependent on the primer trimming .bed file. For the SNAP protocol (snap_primers.bed) we now implement a 5-bp offset, consistent with recommendation from the developers of iVar. For all remaining supported primer sets (not polymerase-based) we do not use the primer offset.
This PR also includes one additional test to verify the parameter's impact on downstream depth of coverage for a test SNAP dataset.
Testing
Tested that when running the workflow with a SNAP dataset and the SNAP .bed file, the primers are trimmed with 5-bp buffer (verified by viewing the primertrimmed.bam file)
Tested that when running the workflow with a non-SNAP (Artic) dataset with the artic .bed file, the primers are trimmed at their true locations without any buffer (verified by viewing the primertrimmed.bam file)
A fix was recently implemented in iVar v. 1.3.1 that addresses an issue with trimming that was identified for some amplicon-based sequencing protocols (e.g. SWIFT, SNAP), where polymerases can add additional bases and lead mismatches.
Prior to this change, the Dockerfile was updated to include this latest version of iVar (https://github.com/chanzuckerberg/idseq-workflows/pull/84). This PR updates the
ivar trimcall in theTrimPrimersstep to leverage the recent change. In particular, it makes theivar trimcommand dependent on the primer trimming .bed file. For the SNAP protocol (snap_primers.bed) we now implement a 5-bp offset, consistent with recommendation from the developers of iVar. For all remaining supported primer sets (not polymerase-based) we do not use the primer offset.This PR also includes one additional test to verify the parameter's impact on downstream depth of coverage for a test SNAP dataset.
Testing