pysam.count ; samtools depyth ; pysam.pileup get differernt results

[Ouhao Lin]

I use samtools depth
pileup with parameter stepper = 'samtools' or 'nofilter'
pysam.count

can you help me to understand the difference? thanks a lot

[Tianran Yao]

你的这个问题跟这个问题（https://groups.google.com/forum/#!topic/pysam-user-group/DBt9exmO_M4）有点类似，对你说不定有启发