filter.rst

augur filter

• How we subsample sequences in the zika-tutoral

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How we subsample sequences in the zika-tutoral

As an example, we'll look that the filter command in greater detail using material form the zika tutorial. The filter command allows you to selected various subsets of your input data for different types of analysis. A simple example use of this command would be

augur filter --sequences data/sequences.fasta --metadata data/metadata.tsv --min-date 2012 --output filtered.fasta

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:

BRA/2016/FC_DQ75D1
COL/FLR_00034/2015
...

To drop such strains, you can pass the name of this file to the augur filter command:

augur filter --sequences data/sequences.fasta \
           --metadata data/metadata.tsv \
           --min-date 2012 \
           --exclude config/dropped_strains.txt \
           --output filtered.fasta

(To improve legibility, we have wrapped the command across multiple lines.) If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the zika tutorial, you should see that one of the sequences in the data set was dropped since its name was in the dropped_strains.txt file.

Another common filtering operation is subsetting of data to a achieve a more even spatio-temporal distribution or to cut-down data set size to more manageable numbers. The filter command allows you to select a specific number of sequences from specific groups, for example one sequence per month from each country:

augur filter \
  --sequences data/sequences.fasta \
  --metadata data/metadata.tsv \
  --min-date 2012 \
  --exclude config/dropped_strains.txt \
  --group-by country year month \
  --sequences-per-group 1 \
  --output filtered.fasta

This subsampling and filtering will reduce the number of sequences in the tutorial data set from 34 to 24.