Mean coverage in Ion Torrent PGM

Question

[Abdul Rafay Khan]

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

Answer 1

[vmicrobio]

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