add quality control steps post variant-calling

[sanjaynagi]

• Things like filtering on depth

• Heterozygosity (Hardy-weinberg)

• Need inspiration for other thresholds, worth looking back at Ag1000G QC steps, or any other AmpSeq pipelines/analyses.

[sanjaynagi]

We need a processing notebook which filters out low quality variants and samples, before running the rest of the analyses. It will need to

• Have sensible, general thresholds, possibly configurable in the config file.
• Store an updated .bed file and metadata file with poor quality samples and variants removed.
• Produce diagnostic plots which can be viewed in the result web book.

[sanjaynagi]

I should begin with simple filters on depth for variants and samples, everything else can come later.

[sanjaynagi]

We have now implemented some basic sample filters (depth, heterozygosity). Closing for now.