Sort Bed

# 2) Sort using reference chromosome order from a FASTA index
sortBed \
  -i variants.vcf \
  -faidx genome.fa.fai \
  -header \
  > variants.sorted.vcf

# 3) Rank features by descending score within chromosome order
sortBed \
  -i peaks.bed \
  -chrThenScoreD \
  > peaks.by-score.bed

Recommended Workflow

1. Decide whether you need true coordinate sorting for downstream interval algorithms or a ranking sort for reporting.
2. Use the default mode for simple chromosome/start sorting, or supply -g / -faidx to impose reference-consistent chromosome order.
3. Add -header if the file contains a header that must remain at the top.
4. If the sorted output will feed a later -sorted bedtools step, verify you used a coordinate sort mode rather than a size/score ranking mode.

Guardrails

• Default chromosome ordering is lexical, so names like chr10 may sort before chr2; use -g or -faidx for reference order.
• -sizeA, -sizeD, -chrThenSizeA, -chrThenSizeD, -chrThenScoreA, and -chrThenScoreD are ranking modes, not substitutes for coordinate-sorted input to chromsweep-based workflows.
• -header only preserves the leading header from the input; it does not infer or reconstruct missing metadata lines.
• Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.