Confirming -T vs -R equivalence for SNP-only BED files (bcftools 1.16)

[gpacinotti]

Hi,

I'm using bcftools 1.16 to extract SNPs from per-scaffold VCFs (generated with biscuit pileup) using matching per-scaffold BED files (generated with biscuit vcf2bed). Command:

bcftools view -T scaffold.bed scaffold.vcf.gz -Oz -o scaffold.snps.vcf.gz

I initially used -R but it was very slow due to random-access seeks for each of the many small intervals in the BED file; switching to -T gave a large speedup.

I've read the manual's explanation of -R/-T, including the note that -r/-R checks both start and end positions of indels while -t/-T checks start positions only. Since my BED files contain only SNPs (single-base intervals), I believe this distinction doesn't apply, so both flags should give identical output, with -T being the better choice here purely for performance reasons (streaming vs. index seeks, given the large number of small intervals).

Could you confirm this reasoning is correct, and that -T is indeed the recommended flag for this use case?

Thanks!