Question: Mean coverage in Ion Torrent PGM
0
gravatar for Abdul Rafay Khan
12 months ago by
Karachi, PK
Abdul Rafay Khan910 wrote:

Is there any way to calculate the mean coverage of each amplicon in a whole run (in 16 or 32 samples)?

coverage ngs ion torrent • 291 views
ADD COMMENTlink modified 12 months ago by vmicrobio240 • written 12 months ago by Abdul Rafay Khan910
1
gravatar for vmicrobio
12 months ago by
vmicrobio240
vmicrobio240 wrote:

Hi Abdul Rafay Khan,

You can use samtools depth:

samtools depth -b file.bed -a file.bam > coverage.csv

Also, a plugin named 'coverageAnalysis' exists directly on the Proton machine

ADD COMMENTlink modified 12 months ago • written 12 months ago by vmicrobio240
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