[Samtools-help] samtools duplicate count

[Ogan <ab...@gm...>]

Dear all,

I have run into something unexpected and maybe someone already knows the 
answer.

I am counting duplicate reads in bam files using 'samtools view -cf 1024 
sample.bam' vs counting lines with 'd' in flag string in 'samtools view 
-X sample.bam' . In the latter case I am getting 1034 less reads out of 
699K duplicate reads. I would have assumed that the numbers would be the 
same.

Is this expected or am I missing something?

Thank you all,

Ogan