ngs-pipeline

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License lacking

1

Thank you so much for sharing this pipeline! I would like to re-use this to build a pipeline to call crispr off target effects. Unfortunately this repository lacks a License...

votti

https://github.com/brentp/somalier

tjbencomo

tjbencomo

It currently has the same values as the WES file. Figure out better resource levels for WGS

tjbencomo

tjbencomo

Right now the pipeline requires sample type be specified as `normal` or `tumor` - the upper case versions cause an error. Call `tolower()` on the `units` data frame in `common.smk`...

tjbencomo

Software like SomaticSniper and VarScan perform the same job as Mutect2. Utilizing many different callers can catch variants that one caller may miss. Results from each caller would be aggregated...

tjbencomo

Set default af-freq for Mutect2 and allow users to specify alternate values in config.yml

1

tjbencomo

tjbencomo

tjbencomo