I have a sorted bedfile comprised of three columns: seqid, start, and end.
sort -k1,1 -k2,2n tmp2.bed > tmp3.bed
1 6589256 6589207 1 11627195 12127194 1 12616616 12116617 1 18283067 18273068 1 21826932 21926931 1 28787213 28788212 1 31195434 31195483 1 39374350 39364351 1 42307024 42357023 1 47379997 47374998
~/tools/bedtools2/bin/bedtools merge -i tmp3.bed
Error: unable to open file or unable to determine types for file tmp3.bed
Probably something silly, but I'm not seeing it.
EDIT:
The second column - start must be before the end coordinates. It would be nice if bedtools threw an informative error as the user sucks.