This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Coverage depth using samtools

Is it correct to use the parameter below to evaluate coverage base per base or is it only going to provide depth?

  samtools depth -a -b

samtools ngs depth sequencing coverage
• 2,371 views • link
written by slzr_ • slzr_

yes but the option -b is missing a file if you want to compute all bases overlapping a bed file.

https://www.htslib.org/doc/samtools-depth.html

-a

    Output all positions (including those with zero depth) 
-a -a, -aa

    Output absolutely all positions, including unused reference sequences. Note that when used in conjunction with a BED file the -a option may sometimes operate as if -aa was specified if the reference sequence has coverage outside of the region specified in the BED file. 
-b FILE

    Compute depth at list of positions or regions in specified BED FILE. []
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

thank you for answering!

even though this parameter shows base-by-base depth from samtools depth, can I say it also reflects coverage across the gene? Since depth per base shows which regions are well or poorly covered, is it correct to make that inference?

• 0 views • link
written by slzr_ • slzr_

you use the term coverage and depth as if they are different things but (to my knowledge) they mean the same thing

• 0 views • link
written by cmdcolin cmdcolin

coverage refers to the percentage of the genome (or target region) that is sequenced at least once, while depth indicates the number of times a particular base is sequenced.

• 0 views • link
written by slzr_ • slzr_

0 answers

No answers yet.

Log in to answer this question.

More posts like this