Question: why did I get 0 at the 3rd column with samtools depth?
gravatar for xjli
2.8 years ago by
xjli0 wrote:

I use "samtools depth bam" but get some zeros at the 3rd column.

  1. It says "positions with zero coverage may be omitted by default" with "samtools depth", why did I still get 0?
  2. Should I use the original bam file or the bam file after mark duplicates and realign the indel region?
  3. Is there any difference between "samtools depth'' and "samtools depth -q 0 -Q 0" in samtools (version 1.3.1)?
  4. How can I do this in multi-threads? I can't figure out the right way of using "nthreads=" Thank you.
coverage samtools alignment • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Devon Ryan88k • written 2.8 years ago by xjli0
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:
  1. "May" is the operative word.
  2. You likely want to run it on the duplicate marked file.
  3. Those are the same. It's not documented, but the defaults are 0 for -q and -Q.
  4. You can't, though you could run samtools depth on different chromosomes in parallel.
ADD COMMENTlink written 2.8 years ago by Devon Ryan88k
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