samtools depth -Q 0 and -Q 1 output discrepancy

[thedamian]

Hi
I have an exons_merged.bed file of total regions length 81036853:

awk 'BEGIN{sum=0}{sum+=$3-$2}END{print sum}' exons_merged.bed
[B]81036853[/B]

Based on this merged BED file I do:

samtools depth -Q 1 -a rmdup.bam -b exons_merged.bed > depth_Q1_MERGED_rmdup.dep

and

samtools depth -a rmdup.bam -b exons_merged.bed > depth_MERGED_rmdup.dep

I use option "-a" because I want to keep ALL positions that are in my BED file
however then I obtain:

wc -l depth_*
  [B]81025877[/B] depth_MERGED_rmdup.dep
  [B]80783802[/B] depth_Q1_MERGED_rmdup.dep

Why non of above numbers are the same like the total number of the bases in BED file? I expected to list all positions from my MERGED.BED file, but instead of I get only some subset...

Why it's like this?

Thanks

[dpryan]

Try "-a -a" rather than "-a" and see if that makes the difference. "-a" alone won't include BED entries that completely lack overlaps, but "-a -a" should.