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Mean coverage in Ion Torrent PGM

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

ion torrent ngs coverage
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updated by vmicrobio vmicrobio • written by Abdul Rafay Khan Abdul Rafay Khan

1 answer

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

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written by vmicrobio vmicrobio

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