Please read the following documentation prior to the discussion:

1. VariantRecalibrator overview for GATK v4.1.2.0
2. Variant Quality Score Recalibration (VQSR) and how it works (includes minimum number of samples required)
3. How to filter variants either with VQSR or by hard-filtering
4. Variant Quality Score Recalibration (VQSR)
5. The variant calling section of Samtools workflows documentation

If you are unfamiliar with scikit-allel, please spend a few minutes familiarizing yourself with the tool. Documentation is available here: https://scikit-allel.readthedocs.io/en/stable/. Specifically, the following tutorials are relevant:

• Tutorial on filtering variants: http://alimanfoo.github.io/2018/04/09/selecting-variants.html
• Tutorial on exploratory analyses for VCF files: http://alimanfoo.github.io/2016/06/10/scikit-allel-tour.html

NOTE: During the discussion we will be looking at some Jupyter notebooks from the Morrell Lab that uses scikit-allel to explore VCF files to identify a set of VCF filtering criteria. We will also take a brief look at plots of bcftools stats.