annot-tsv

name	annot-tsv
description	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.
disable-model-invocation	true
user-invocable	true

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)