How to find the non-mapped regions against a reference genome?

[rubyb]

Dear all,
I'm working on NGS data (HiSeq Illumina). After filtering the quality on my fastq data files . I have mapped my reads against a reference genome using bwa. I then generated a sam alignment file (sam then bam) and a vcf (containing the coordinates of my snps & indels) file using respectively bwa,samtools & bcftools.

I would like to know if there is any software capable of giving the coordinates of the regions where the reads are not mapping the reference? (consensus sequences)
Or do you have any idea how to get them?
Thank you .

[zhidkov.ilia]

Hi rubyb,
you can generate pileup file from sam/bam file and then look for not continuous numbers correspond to positions in reference sequence. For example:
chr1 333 A 10 …..,,,,, IIIII
chr1 555 G 10 …..,,,,, IIIII

the region between positions 333 and 555 in chr1 was not covered.

Ilia

[rubyb]

thank you very much!
i'm going to try it =)