This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
However, I was tinkering with ViReflow, and I noticed that this samtools depth command is missing a critical argument: -J (Include reads with deletions in depth computation). I think this might be the culprit behind the "bcftools consensus bug" Kristian had told us about in the past: by omitting -J, we are accidentally undercounting the coverage at sites in which reads have deletions. In my experimentation, simply adding -J completely fixes this. Thus, I propose we (urgently) change our samtools depth command to the following:
Currently, we run
samtools depthlike this:We got this from the Andersen lab pipeline:
However, I was tinkering with ViReflow, and I noticed that this
samtools depthcommand is missing a critical argument:-J(Include reads with deletions in depth computation). I think this might be the culprit behind the "bcftools consensus bug" Kristian had told us about in the past: by omitting-J, we are accidentally undercounting the coverage at sites in which reads have deletions. In my experimentation, simply adding-Jcompletely fixes this. Thus, I propose we (urgently) change oursamtools depthcommand to the following: