CLI Reference

CLI Reference#

GATAC ships a command-line interface for the preprocessing pipeline. Every step that turns raw fragment files into analysis-ready matrices is available as a sub-command.

gatac [--verbose] <command> [options]

Global option:

Flag

Description

-v, --verbose

Enable debug-level logging

Commands at a glance#

convert

Convert TSV.GZ fragment files to Parquet.

gatac convert
metrics

Compute TSS enrichment and fragment QC statistics.

gatac metrics
filter

Filter barcodes by quality thresholds.

gatac filter
doublets

Detect doublet / multiplet cells (AMULET Poisson method).

gatac doublets
tile

Build a cell × genomic-tile count matrix.

gatac tile
gene

Build a cell × gene activity matrix.

gatac gene
genescore

Build an ArchR-style distance-weighted gene score matrix.

gatac genescore
features

Select highly accessible features.

gatac features
combine

Merge multiple h5ad files into one.

gatac combine