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??
Thanks for the quick response! my reads are indeed paired, when you say that the alignment is not marked as proper pair you mean this is not properly marked in the bam file, right?
correct, add the
flag and see if that fixes it, the next best quess is the BAQ cutoff.
Alternatively, filter your BAM file for the location in question and look at the alignment properties over that location.