amalgkit csfilter

Overview

amalgkit csfilter performs cross-species outlier filtering using ortholog information and writes filtered metadata plus cross-species QC plots. It is Python-only.

Required input

• filtered or unfiltered metadata.tsv
• merge or cstmm output directory via --input_dir
• one of:
  • --dir_busco
  • --orthogroup_table

Example

amalgkit csfilter --out_dir ./ --dir_busco ./busco

Main outputs

• csfilter/metadata.tsv
• csfilter/excluded.tsv
• csfilter/csfilter_exclusion.pdf
• csfilter/csfilter_overview.pdf
• csfilter/csfilter_unaveraged_pca_PC12.pdf
• csfilter/csfilter_heatmap.pdf
• csfilter/csfilter_within_group_cor.pdf
• csfilter/csfilter_outlier_scatter.pdf

Useful options

• --missing_strategy em_pca|nipals|row_mean
• --margin_threshold
• --robust_z_threshold

Typical chaining

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 sva