Remove redundant include strains #843
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Removes older references from the list of strains to force include in analyses. We use the single Wuhan/Hu-1/2019 strains as the reference for alignment and time tree rooting, so the other two strains are not required. Importantly, these additional strains get used in proximity calculations with priority-based subsampling leading to the unexpected inclusion of contextual strains that look like these redundant root sequences. We try to avoid this problem in the proximity calculations by defining a list of strains to ignore [1], but this list only includes the strain used to root the time tree. Rather than updating this list to include more strains, we can just remove the strains from the include file. [1] https://github.com/nextstrain/ncov/blob/51ac8143761057c14de3841e46b82e08f7fef4b6/workflow/snakemake_rules/main_workflow.smk#L372
Defines a list of strains to ignore, including the two reference sequences we use for GISAID and GenBank builds and passes this list to the `ignore_seqs` parameter of the proximity calculations instead of the current build's root sequence alone.
cassiawag
reviewed
Jan 25, 2022
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I tested this out on ncov-kenya, and the proximity sequences & priority scores were as expected. Thanks @huddlej!
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@rneher Does this look ok to you, too? This bit of the workflow is just complicated enough that I can imagine I'm missing something with this change... |
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Description of proposed changes
Removes older references from the list of strains to force include in
analyses. We use the single Wuhan/Hu-1/2019 strains as the reference for
alignment and time tree rooting, so the other two strains are not
required. Importantly, these additional strains get used in proximity
calculations with priority-based subsampling leading to the unexpected
inclusion of contextual strains that look like these redundant root
sequences. We try to avoid this problem in the proximity calculations by
defining a list of strains to ignore, but this list only includes
the strain used to root the time tree. Rather than updating this list to
include more strains, we can just remove the strains from the include
file.
Testing