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fixup! Update existing examples
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Rename exclude file to exclude.txt
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victorlin committed Feb 26, 2024
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6 changes: 3 additions & 3 deletions docs/usage/cli/filter.rst
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Expand Up @@ -36,23 +36,23 @@ A simple example use of this command would be
This command will select all sequences with collection date in 2012 or later.
The filter command has a large number of options that allow flexible filtering for many common situations.
One such use-case is the exclusion of sequences that are known to be outliers (e.g. because of sequencing errors, cell-culture adaptation, ...).
These can be specified in a separate file:
These can be specified in a separate text file (e.g. ``exclude.txt``):

.. code-block::
BRA/2016/FC_DQ75D1
COL/FLR_00034/2015
...
To drop such strains, you can use ``--exclude``:
To drop such strains, you can pass the filename to ``--exclude``:

.. code-block:: bash
augur filter \
--sequences data/sequences.fasta \
--metadata data/metadata.tsv \
--min-date 2012 \
--exclude config/dropped_strains.txt \
--exclude exclude.txt \
--output-sequences filtered_sequences.fasta \
--output-metadata filtered_metadata.tsv
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