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Use mutations rather than mutations-per-site for clade IIb/B.1 builds #230

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merged 2 commits into from
Jan 20, 2024
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Use mutations rather than mutations-per-site for clade IIb/B.1 builds #230

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5ae7e57
Use mutations rather than mutations-per-site for clade IIb/B.1 builds
corneliusroemer Jan 20, 2024
4c7fddd
fix: add divergence_units also to ci profile
corneliusroemer Jan 20, 2024
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1 change: 1 addition & 0 deletions phylogenetic/config/hmpxv1/config.yaml
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Expand Up @@ -70,6 +70,7 @@ timetree: true
root: "MK783032 MK783030"
clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

## recency
recency: true
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1 change: 1 addition & 0 deletions phylogenetic/config/hmpxv1_big/config.yaml
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Expand Up @@ -49,6 +49,7 @@ timetree: true
root: "OP890401"
clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

## recency
recency: true
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1 change: 1 addition & 0 deletions phylogenetic/config/mpxv/config.yaml
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Expand Up @@ -66,6 +66,7 @@ timetree: false
root: "min_dev"
clock_rate: 3e-6
clock_std_dev: 6e-6
divergence_units: "mutations-per-site"

## recency
recency: true
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1 change: 1 addition & 0 deletions phylogenetic/profiles/ci/builds.yaml
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Expand Up @@ -73,6 +73,7 @@ timetree: true
root: "MK783032 MK783030"
clock_rate: 5.7e-5
clock_std_dev: 2e-5
divergence_units: "mutations"

## recency
recency: true
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3 changes: 2 additions & 1 deletion phylogenetic/workflow/snakemake_rules/core.smk
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Expand Up @@ -221,7 +221,6 @@ rule refine:
- use {params.coalescent} coalescent timescale
- estimate {params.date_inference} node dates
- filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
Note: --use-fft was removed (temporarily) due to https://github.com/neherlab/treetime/issues/242
"""
input:
tree=rules.fix_tree.output.tree
Expand All @@ -244,6 +243,7 @@ rule refine:
if "clock_std_dev" in config
else "",
strain_id=config["strain_id_field"],
divergence_units=config["divergence_units"],
shell:
"""
augur refine \
Expand All @@ -263,6 +263,7 @@ rule refine:
--coalescent {params.coalescent} \
--date-inference {params.date_inference} \
--date-confidence \
--divergence-units {params.divergence_units} \
--clock-filter-iqd {params.clock_filter_iqd}
"""

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