Question: defintion of extremely low coverage
0
gravatar for statfa
2.8 years ago by
statfa410
statfa410 wrote:

hi,

I have searched for the answer but I still need more clear explanation to understand the concept.

we need to filter out exons that have extremely low coverage (median read depth across all samples less than 20, which mostly reflect capture failure).

As I know, the concept of coverage depth is different from read depth... coverage depth simply means how much each segmentation is covered by the sequencing platform. While read depth means how many times a segmentation has been read. (please correct me if I'm wrong).

now my question is how can "extremely low coverage" be defined as "median read depth across all samples less than 20"?

could someone give me a clear explanation of "median" read depth?

Thank you so much

coverage read depth • 977 views
ADD COMMENTlink modified 2.8 years ago by igor7.4k • written 2.8 years ago by statfa410
3
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:
  1. Count the number of reads per region in each sample.
    • Be sure to filter out anything that's excluded by your variant caller.
  2. Take the median per region across samples
  3. Filter
ADD COMMENTlink written 2.8 years ago by Devon Ryan88k

Thank you so much... I appreciate that.

ADD REPLYlink written 2.8 years ago by statfa410
3
gravatar for igor
2.8 years ago by
igor7.4k
United States
igor7.4k wrote:

For most people, coverage and read depth are the same. If a certain nucleotide has 10 reads overlapping it, then the coverage for it is 10X. A region of interest (a single exon or an entire exome) has multiple nucleotides. Each nucleotide has a specific coverage value. You can take a median of those to get the median coverage.

Also, you can use something like GATK DepthOfCoverage to do the calculation for you: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by igor7.4k
1

I always thought "depth" meant the average number of reads above any given base, and "coverage" meant the amount of genome with at least 1 read covering it..?

ADD REPLYlink written 2.8 years ago by John12k
2

That can be the case, but isn't always. It's a lovely ambiguous language we speak.

ADD REPLYlink written 2.8 years ago by Devon Ryan88k
1

Yes I suppose "number of times the base is covered by reads" is also depth. Perhaps we should all switch to unambiguous emojis for technical talk. Like:

"All technical 🐑🐑 were 🔬 and found to have a ♨️ and 🍉 leading us to 🤔 that 👾 🛀 🎱 🎻."

Just kidding, that makes no sense - but only because the Unicode Consortium hasn't accepted an application for read depth and genomic coverage emojis... yet.

ADD REPLYlink written 2.8 years ago by John12k
1

Then we'd have problems like just now, where I can only see one of the emojis... :P

ADD REPLYlink written 2.8 years ago by Devon Ryan88k

Thank you so much for the information... I appreciate that.

ADD REPLYlink written 2.8 years ago by statfa410
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