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Question: Computing coverage from BAM file?
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gravatar for maryamom99
3.3 years ago by
maryamom99 • 0
maryamom99 • 0 wrote:

Hi every one!

I want to compute depth of specific regions from BAM file.I found two solutions like bellow :

samtools depth -r  <region>  my.bam     

and 

samtools view my.bam <region>

that give me two different answers,I was wondering what is exactly the applications of theses two command and which one is more correct answer to computing depth of region?

Thanks a lot!
bam depth covrage • 1.3k views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by maryamom99 • 0
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gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

http://www.htslib.org/doc/samtools.html

"view" will report all data within a particular region
"depth" is the how many reads at the particular position

You might find the tool BEDTools -> Create a BedGraph of genome coverage a useful alternative.

Best, Jen, Galaxy team

 
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jennifer!

ADD REPLY • link written 3.3 years ago by maryamom99 • 0
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