So I ran Mpileup on a Bam file i generated, I run the command:
samtools mpileup -f hg19.fa file1.bam -o file1_pileup.txt
But when I look at this pileup file, it looks like samtools skips certain positions:
chr19 1080247 N 2 cc EE chr19 1080257 N 2 cc AA chr19 1080258 N 2 c$c AA chr19 1080259 N 1 a$ A chr19 1185895 N 1 ^]C A chr19 1185896 N 1 G A
and when I load the original file1.bam in IGV browser I can clearly see there are reads in the are between 1080259 and 1185895. Using Mpileup without refrence file doesn't change anything...
Does anybody have an idea how this happends or how I can fix this??