Orientation Bias Filters

[maotian06]

Hi all,

Here, we are trying to add a new filter function to filter out the orientation bias using GATK's LearnReadOrientationModel.

The read orientation bias is the bias that occurs during library preparation or sample processing. The most common biases are:

1. library preparation: G -> T
2. FFPE samples: C -> T.

When compared with the pipeline without the LearnReadOrientationModel function, I found little difference in the stimulated samples A-full-P2, but ~10% difference in the real FFPE sample.

#61

[maotian06]

@tyamaguchi-ucla @yashpatel6 @stefaneng @rhughwhite @jmlivingstone @zhuchcn
Mind to test it out? But I haven't merge it to the main, so might need to use the branch maotian-add-LearnReadOrientationModel

[tyamaguchi-ucla]

Were you wondering if this filter might over filter SNVs (even TPs)?