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diriano / ploidyNGS

Explore ploidy levels from NGS data alone
GNU General Public License v3.0
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Min cov update #17

Closed novigit closed 2 years ago

novigit commented 2 years ago

Hi! The main change is a new option, --min_cov. It allows to user to set a coverage threshold for alignment positions to be considered. The default value is 0, so not calling the option returns the same behavior as the original script.

This option can be useful to determine whether 50/50, 33/67, etc peaks in your histogram are the result of sequencing errors in low coverage regions in your BAM file. In our case, setting a --min_cov 10 let to a complete vanishing of these noisy peaks.

The pull request also contains a few other minor fixes and suggestions. See comments of these commits for more details

diriano commented 2 years ago

These are great improvements. Thanks @novigit . Will add them to main.