Discrepancy between samtools depth and Sambamba region

[wynstep]

Dear all, I am finding a big discrepancy in the calculation of BAM depth for a whole chromosome (chr4 in this example).

If I run the samtools command: samtools depth -a -r "chr4:0-191154275" 111056.bam | awk '{sum+=$3} END { print "Average = ",sum/191154275 I obtain the result: Average = 24.5936

BUT if I run the command with Sambamba: sambamba depth region -L "chr4:1-191154276" -t 10 -F '' -c 0 111056.bam I obtain: chr4 0 191154276 49213637 2.32988 111056

Am I doing something wrong? Could you please help me?

Sambamba version: 0.7.1 Unfortunately I cannot attach the file because it's too big, but I can do tests for you very rapidly.

[pjotrp]

Have a look at the raw data and tell us what you see.

[pjotrp]

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