bam-readcount total count differs from igv total count

[aury98]

Hi, I’m asking why the total count of IGV differs from the total count of bam-readcount.
As you can see the total count on IGV is 8827+9462=18289, while the total count with bam-readcount is 18276.

[chrisamiller]

Typically, this has to do with the settings on which reads are shown and filtered. See this comment for more information:
#46

bam readcount is equivalent to samtools view -F 1796