Hello, I am a beginner and trying to understand samtools.
I have no problem getting samtools to do what I want, I have trouble interpreting the results and the different fields in the format. For instance when I say :
samtools view file.bam chr20:628200-628400
Why do I get a value with position values equal to : 628004-628107?
This is obviously not in my specified range so why did it come up?
Second question, the "length" column in samtools is not equal to the actual length of my sequence. It can range anywhere from -202 and 173, but my reads are all 100bp.
I am ever grateful because this has been driving me totally insane.