Question: why did I get 0 at the 3rd column with samtools depth?
gravatar for xjli
3.4 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 • 1.3k views
ADD COMMENTlink modified 3.4 years ago by Devon Ryan92k • written 3.4 years ago by xjli0
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k 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 3.4 years ago by Devon Ryan92k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1741 users visited in the last hour