mask-fasta-from-bed

name	mask-fasta-from-bed
description	Use when you need to hard-mask or soft-mask regions in a FASTA file using BED, GFF, or VCF coordinates, such as repetitive elements, blacklist regions, or loci to exclude from sequence analysis.
disable-model-invocation	true
user-invocable	true

mask-fasta-from-bed

Quick Start

• Command: maskFastaFromBed -fi <input.fasta> -bed <intervals.bed> -fo <output.fasta>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/maskFastaFromBed
• Full reference: See references/help.md

When To Use This Tool

• Hard-mask repetitive, blacklisted, or excluded regions in a FASTA with N or another replacement character.
• Soft-mask regions by lowercasing the existing sequence with -soft.
• Apply interval masks from BED, GFF, or VCF files to a reference or contig FASTA.
• Produce a derived masked FASTA without changing the original source file.

Common Patterns

# 1) Hard-mask listed regions with Ns
maskFastaFromBed \
  -fi genome.fa \
  -bed blacklist.bed \
  -fo genome.masked.fa

# 2) Soft-mask repeats by converting bases to lowercase
maskFastaFromBed \
  -fi genome.fa \
  -bed repeats.bed \
  -fo genome.softmasked.fa \
  -soft

# 3) Hard-mask with a custom replacement character and full FASTA headers
maskFastaFromBed \
  -fi contigs.fa \
  -bed mask-regions.bed \
  -fo contigs.masked.fa \
  -mc X \
  -fullHeader

Recommended Workflow

1. Confirm the interval file uses the same sequence naming convention as the FASTA headers.
2. Choose hard masking (default), soft masking with -soft, or an alternate hard-mask character with -mc.
3. Write the result to a new FASTA via -fo and preserve the original FASTA as the unmasked source.
4. Spot-check a few loci to confirm the intended regions were masked and the header matching behaved as expected.

Guardrails

• -fo is required; this tool does not modify the input FASTA in place.
• Default behavior replaces masked sequence with uppercase N; -soft instead lowercases the original bases.
• -mc changes the hard-mask character; it is not a substitute for -soft.
• By default bedtools matches only the first token of a FASTA header; use -fullHeader when interval names must match the entire header line.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.