coverage per position - less positions than in reference

[boetsie]

Hi all,

i have a question concerning the coverage per position. I have a sorted .bam file which i use to determine the coverage per position. I use the code;

samtools pileup -f reference.fa bamfile.bam > coverageperposition.txt

when i check the number of lines, I get 4.543.383 positions. My reference is 4.639.675 bp long. So i'm missing around 100.000 positions!

Another method I used is with BEDTools;

genomeCoverageBed -ibam bamfile.bam -g genome.txt -bga > coverageperpositionBEDTOOLS.txt

if i check here the number of lines, I get only 3.429.006 positions!

Am i doing something wrong here? How can i get for every position in the genome the coverage? I need this, because I want to plot the coverage in a graph, along with the genome. So the number of positions should match the size of the genome.

Kind regards,
Boetsie