amalgkit wsfilter

Overview

amalgkit wsfilter performs within-species outlier filtering. It writes filtered metadata, excluded-row summaries, and per-species QC plots.

wsfilter is Python-only.

Inputs

wsfilter expects:

• metadata from metadata, integrate, select, or a previous filter step
• abundance tables from merge or cstmm

If --input_dir inferred is used, AMALGKIT reads:

out_dir/cstmm if it exists, otherwise out_dir/merge

If --metadata inferred is used, AMALGKIT can reuse the newest prior filter metadata when available:

out_dir/wsfilter/metadata.tsv
out_dir/csfilter/metadata.tsv
out_dir/metadata/metadata.tsv

For the first filter pass, an explicit metadata path is often clearest:

amalgkit wsfilter --out_dir ./ --metadata ./metadata/metadata.tsv

Basic Use

amalgkit wsfilter --out_dir ./

Restrict to selected sample groups:

amalgkit wsfilter \
    --out_dir ./ \
    --sample_group leaf,root,flower

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

Option	Default	Use
--mapping_rate	0.2	mapping-rate cutoff
--dist_method	pearson	distance/correlation method
--norm	log2p1-fpkm	expression transformation before filtering
--margin_threshold	0.0	robust-margin threshold
--robust_z_threshold	-2.5	robust z-score threshold
--one_outlier_per_iter	no	remove at most one outlier per group/project per iteration
--plot_intermediate	no	write intermediate filtering plots

Chaining

Use only within-species filtering:

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

Continue to 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