Question: why did I get 0 at the 3rd column with samtools depth?
2.8 years ago by
xjli • 0
xjli • 0 wrote:
I use "samtools depth bam" but get some zeros at the 3rd column.
- It says "positions with zero coverage may be omitted by default" with "samtools depth", why did I still get 0?
- Should I use the original bam file or the bam file after mark duplicates and realign the indel region?
- Is there any difference between "samtools depth'' and "samtools depth -q 0 -Q 0" in samtools (version 1.3.1)?
- How can I do this in multi-threads? I can't figure out the right way of using "nthreads=" Thank you.
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