amalgkit wsfilter

Overview

amalgkit wsfilter performs within-species outlier filtering and writes filtered metadata plus per-species QC plots. It is Python-only.

Input

• --metadata: metadata table from amalgkit metadata or amalgkit integrate
• --input_dir: merge or cstmm output directory

If --metadata inferred is used, wsfilter automatically picks the newest of:

• out_dir/wsfilter/metadata.tsv
• out_dir/csfilter/metadata.tsv
• otherwise out_dir/metadata/metadata.tsv

Example

amalgkit wsfilter --out_dir ./

Main outputs

• wsfilter/metadata.tsv
• wsfilter/excluded.tsv
• wsfilter/wsfilter_exclusion.pdf
• wsfilter/<Species>/<Species>_within_group_correlation_no.pdf
• wsfilter/<Species>/<Species>_tau_histogram_no.pdf

Useful options

• --mapping_rate
• --dist_method
• --margin_threshold
• --robust_z_threshold
• --plot_intermediate yes|no

Typical chaining

amalgkit wsfilter --out_dir ./
amalgkit finalize --out_dir ./ --metadata ./wsfilter/metadata.tsv --batch_effect_alg no

With cross-species filtering:

amalgkit wsfilter --out_dir ./
amalgkit csfilter --out_dir ./ --metadata ./wsfilter/metadata.tsv --dir_busco ./busco
amalgkit finalize --out_dir ./ --metadata ./csfilter/metadata.tsv --batch_effect_alg latent_glm