remove-dup

name	remove-dup
description	Use when removing duplicate alignments from SAM or BAM files with the Subread `removeDup` CLI and a location-count cutoff.
disable-model-invocation	true
user-invocable	true

remove-dup

Subread binary for duplicate-read removal. It reads SAM or BAM, groups reads by mapped location, and drops every read at locations whose depth meets or exceeds the configured duplication threshold.

Quick Start

• Command: removeDup -i <input.sam|bam> -o <output.bam>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/removeDup
• Default duplication cutoff: 10

When To Use This Tool

• Removing dense duplicate alignments from mapped read files before downstream counting or QC
• Applying a simple location-based duplication filter to SAM or BAM without marking duplicates first
• Forcing SAM output with -S when a downstream step cannot read BAM
• Running a quick Subread-native duplicate purge rather than a more feature-rich deduplication workflow

Common Patterns

# Write BAM output with the default cutoff
removeDup -i alignments.bam -o dedup.bam

# Tighten the removal threshold
removeDup -i alignments.sam -o dedup.bam -r 2

# Emit SAM instead of BAM
removeDup -i alignments.bam -o dedup.sam -S

Recommended Workflow

1. Start from a valid SAM or BAM alignment file.
2. Decide whether the default cutoff of 10 is acceptable; lower it only if you intentionally want aggressive pruning.
3. Write BAM by default, or add -S only when plain-text SAM is required downstream.
4. Inspect the summary banner or view the output with samtools view to confirm how many reads actually survived.

Guardrails

• -h and --version are not true metadata/help switches; both are treated as invalid options, then the binary prints its usage banner and continues to complain about missing or invalid input.
• In live testing, three reads at the same locus with -r 2 caused all three reads to be removed, confirming this tool drops the entire location bucket once the cutoff is reached.
• The usage text says output is BAM unless -S is specified, even though the -o description loosely says “output SAM file.”
• The tool requires -i and -o; invoking it without a real SAM/BAM input ends in ERROR: The input file is neither a BAM file nor a SAM file.
• This is a blunt duplicate filter, not a marker: it does not preserve one representative read at over-threshold loci.