Closed sanjaynagi closed 6 months ago
We need a processing notebook which filters out low quality variants and samples, before running the rest of the analyses. It will need to
I should begin with simple filters on depth for variants and samples, everything else can come later.
We have now implemented some basic sample filters (depth, heterozygosity). Closing for now.
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.