htsfile

name	htsfile
description	Use when you need to identify, view, or copy HTS-format files (BAM, CRAM, VCF, BCF). Use for inspecting file headers or viewing textual representations of binary HTS files.
disable-model-invocation	true
user-invocable	true

htsfile

Quick Start

• Command: htsfile [OPTIONS] FILE...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/htsfile
• Version: 1.22.1
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Quickly identify whether a file is BAM, CRAM, VCF, BCF, or another HTSlib-supported format.
• View the text form or just the header of a binary HTS file.
• Debug “what format is this file actually?” problems before using heavier tools.
• Use it as a lightweight probe, not a full analysis step.

Common Patterns

# 1) Identify file type
htsfile sample.bam

# 2) Show only the header
htsfile -c -h sample.bam

# 3) View textual representation
htsfile -c sample.bcf

# 4) Copy exact contents
htsfile --copy sample.bam sample.copy.bam

Recommended Workflow

1. Use htsfile first when file-type confusion is blocking the workflow.
2. Switch to samtools or bcftools once the file type is confirmed.
3. Use header-only viewing when you just need metadata and not the full text dump.
4. Keep it as a diagnostic helper in scripts that need early format validation.

Guardrails

• --copy is a dedicated mode and requires one source plus one destination.
• -h and -H mean opposite things in view mode.
• htsfile is for inspection and diagnosis, not rich editing or filtering.
• Text view of large files can be enormous, so prefer header-only mode when possible.

Guardrails

• The --copy subcommand requires exactly one source FILE and one DESTFILE
• Options -h (header-only) and -H (no-header) have opposite effects in view mode
• Verbosity increases with -v; use for additional diagnostics and warnings