Bedtools intersect 0- and 1-based coordinate files

Question

[maxrwjones]

Hi all,

I'm using bedtools intersect for the first time and am wondering if it performs correctly when provided with an 'A' (query) file in BAM format (which has 0-based coordinates) and a 'B' (reference) file in GFF3 format (which has 1-based coordinates).

Does bedtools intersect automatically take this difference into account? i.e. can it re-coordinate one of the files on the fly to ensure intersects are accurate to nucleotide resolution?

Cheers!

Answer 1

[ATpoint]

Does bedtools intersect automatically take this difference into account?

Yes, it is quite a smart one.

Example (BED vs GTF, random files I had on disk):

$ cat test.gtf 
chr1    rtracklayer exon    1   2   .   +   .   exon_id "ENSMUSE00001343744.1"; exon_rank 1; transcript_id "ENSMUST00000193812.1"; gene_id "ENSMUSG00000102693.1"; ID "ENSMUST00000193812.1"

$ cat test.bed 
chr1    0   1   featureA    .   +

$ bedtools intersect -a test.bed -b test.gtf 
chr1    0   1   featureA    .   +

[maxrwjones]

Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.