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Old 02-20-2017, 05:03 PM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
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I've forgotten how SnpEff outputs information, but in general using 'grep -c' is a quick (but mostly manual) way.

If you want to count lots of things at once, isolate out the categories (e.g. using 'cut'), then run 'sort' and 'uniq -c'. Alternatively, import the data into R and use 'table'.
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