Mysterious parameters for plot-covg-hist.R script

mcveanlab / mccortex

De novo genome assembly and multisample variant calling

https://github.com/mcveanlab/mccortex/wiki

MIT License

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Mysterious parameters for plot-covg-hist.R script #68

Closed mbhall88 closed 6 years ago

mbhall88 commented 6 years ago

In the workflow examples for plotting coverage distribution you give an example of running this plot with

scripts/plot-covg-hist.R covg.before_cleaning.csv covg.before_cleaning.pdf

However, when I do this I get an error saying I am missing two parameters [<cutoff> [<kcov>]]. What do these mean/do? Would be great if you could add a passage about this in the wiki.

noporpoise commented 6 years ago

The last two arguments were supposed to be optional but were required by a bug. They should now be optional again (git pull to get fixed version).

cutoff is the cleaning cutoff used/proposed
kcov is approximate kmer coverage of your sample (see https://github.com/mcveanlab/mccortex/wiki/Kmer-coverage)