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.
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