[Samtools-help] mpileup -l BED region file 0-based problem

[Guillermo M. P. <gui...@si...>]

Hello,

I'm using samtools  1.2 using htslib 1.2.1. When using mpileup and using 
option "-l" with a BED file (following UCSC format, 
http://genome.ucsc.edu/FAQ/FAQformat.html#format1 BED file is 0 based).

So the following bed with mpileup:

chr17    41249260    41249306

should limit output to positions [41249260, 41249306[ = 41249260 to 
41249305.
However I'm getting pileup information ]41249260, 41249306] = 41249261 
to 41249306.

I know this issue was reported in older samtools versions and the answer 
was "BED format isn't supported by samtools". Is samtools still not 
supporting BED format? Is this a bug?

I know I could subtract 1 to each start and end coordinate of the BED 
file, but then I won't be a standard BED 0-based file. Is there any 
solution to this?

Thank you.

Best regards,
Guillermo.