How do I install the Annot Tsv skill?

Run npx skillmds add vimalinx/annot-tsv in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Annot Tsv safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Annot Tsv?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Annot Tsv free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Annot Tsv?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Annot Tsv by vimalinx — Agent Skill

Name: Annot Tsv
Rating: 4.2 (5 reviews)
Author: vimalinx

Annot Tsv

Use when you need to annotate regions in a target TSV/BED file with information from overlapping regions in a source file, transfer columns between files based on genomic overlap, or filter/drop overlapping records.

vimalinx c97da93 2 files · 6.9 KB Updated Sep 9, 2026 0 repo stars

File contents

annot-tsv

CLI tool from htslib (1.22.1) that annotates regions in a target file using overlapping regions from a source file. Supports column transfer, conditional matching, special annotations (count, fraction, base pairs), and grep-like filtering. Coordinates are 1-based and inclusive by default.

Quick Start

Command: annot-tsv -s source.txt -t target.txt -c chr,beg,end -f info:INFO > output.txt
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/annot-tsv
Full reference: See references/help.md for complete options and examples

When To Use This Tool

Transferring annotation columns from a source file to overlapping regions in a target file
Filtering records by overlap (print matching lines or drop overlapping regions with -x)
Adding overlap statistics: count of overlapping regions (cnt), fraction overlapped (frac), or base pairs overlapped (nbp)
Conditional annotation transfer requiring matching values in specified columns (-m)

Common Patterns

# 1) Transfer INFO from overlapping source regions into the target table
annot-tsv \
  -s source.txt \
  -t target.txt \
  -c chr,beg,end \
  -f info:INFO \
  > output.txt

# 2) Require matching type/sample columns before annotation transfer
annot-tsv \
  -s src.txt.gz \
  -t tgt.txt.gz \
  -c chr,beg,end \
  -m type,sample \
  -f info

# 3) Use grep-like overlap filtering instead of column transfer
annot-tsv \
  -s source.txt \
  -t target.txt \
  -c chr,beg,end \
  -x

Recommended Workflow

Identify the chromosome, start, and end column names/indices in both source and target files
Determine which columns to transfer (-f) and any required match conditions (-m)
Run a test annotation with a subset to verify column mapping and output format
Execute the full annotation, redirecting stdout to output file or using -o

Guardrails

Coordinates are 1-based and inclusive by default; use -C to specify different conventions (e.g., BED is 0-based start)
Either source or target can be streamed from stdin, but not both simultaneously
The -x (drop overlaps) option is incompatible with -f (column transfer)
Use --help, not -h, for usage output. Here -h is the header-row option and requires an argument.

---name: annot-tsvdescription: Use when you need to annotate regions in a target TSV/BED file with information from overlapping regions in a source file, transfer columns between files based on genomic overlap, or filter/drop overlapping records.--- # annot-tsv CLI tool from htslib (1.22.1) that annotates regions in a target file using overlapping regions from a source file. Supports column transfer, conditional matching, special annotations (count, fraction, base pairs), and grep-like filtering. Coordinates are 1-based and inclusive by default. ## Quick Start - **Command**: `annot-tsv -s source.txt -t target.txt -c chr,beg,end -f info:INFO > output.txt` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/annot-tsv` - **Full reference**: See `references/help.md` for complete options and examples ## When To Use This Tool - Transferring annotation columns from a source file to overlapping regions in a target file - Filtering records by overlap (print matching lines or drop overlapping regions with `-x`) - Adding overlap statistics: count of overlapping regions (`cnt`), fraction overlapped (`frac`), or base pairs overlapped (`nbp`) - Conditional annotation transfer requiring matching values in specified columns (`-m`) ## Common Patterns ```bash # 1) Transfer INFO from overlapping source regions into the target table annot-tsv \ -s source.txt \ -t target.txt \ -c chr,beg,end \ -f info:INFO \ > output.txt ``` ```bash # 2) Require matching type/sample columns before annotation transfer annot-tsv \ -s src.txt.gz \ -t tgt.txt.gz \ -c chr,beg,end \ -m type,sample \ -f info ``` ```bash # 3) Use grep-like overlap filtering instead of column transfer annot-tsv \ -s source.txt \ -t target.txt \ -c chr,beg,end \ -x ``` ## Recommended Workflow 1. Identify the chromosome, start, and end column names/indices in both source and target files 2. Determine which columns to transfer (`-f`) and any required match conditions (`-m`) 3. Run a test annotation with a subset to verify column mapping and output format 4. Execute the full annotation, redirecting stdout to output file or using `-o` ## Guardrails - Coordinates are 1-based and inclusive by default; use `-C` to specify different conventions (e.g., BED is 0-based start) - Either source or target can be streamed from stdin, but not both simultaneously - The `-x` (drop overlaps) option is incompatible with `-f` (column transfer) - Use `--help`, not `-h`, for usage output. Here `-h` is the header-row option and requires an argument.

Frequently asked questions