coordinates in alignment

[m_elena_bioinfo]

Hi NGS user,
I have a question about alignment
Is there any method to find the coordinates in the genome in which there are not reads?

For example, I'm using Bio:B::Samtools to extract position in reference file in which reads are mapped.
But I can't extract the position of reference region in which there are not reads.
Someone could help me?

Thanx a lot!
Mary Hellen

[adamdeluca]

look at the complementBed program in bedtools

http://code.google.com/p/bedtools/