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.
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Update QC cutoffs for samples to include when building trees and run stringent only #125
From: "Laurent, Louise"
Date: Friday, September 24, 2021 at 5:15 PM
Subject: Re: Should sample qc criteria for tree-building and/or variant/epidemiology usability be updated?
As noted by Amanda, the "overall_fail" column takes into account the N-metric, which adds a substantial layer of stringency. My reasoning is this:
• for return of results into the medical record, we want to be very stringent (so use "overall_fail").
• for building trees, we can afford to be less stringent (so use "any_fail") and it may be of benefit to include more samples.
Louise
From: "Laurent, Louise" Date: Friday, September 24, 2021 at 5:15 PM Subject: Re: Should sample qc criteria for tree-building and/or variant/epidemiology usability be updated?
As noted by Amanda, the "overall_fail" column takes into account the N-metric, which adds a substantial layer of stringency. My reasoning is this: • for return of results into the medical record, we want to be very stringent (so use "overall_fail"). • for building trees, we can afford to be less stringent (so use "any_fail") and it may be of benefit to include more samples. Louise