Intro-to-variant-analysis

Intro-to-variant-analysis copied to clipboard

Pick a new dataset

2

I think we can get a better dataset than the DREAM dataset https://www.nature.com/articles/s41597-021-01077-5#code-availability

Gammerdinger

Gammerdinger

maybe a tree command check before AlignmentQC

2

A check list to make sure people have the correct files for multiQC

mistrm82

currently PoN file is listed as being in the reference; we will have to add it there for students to have on hand, or direct them to download it from...

hwick

Move MultiQC after we have run SnpEff

Gammerdinger

PoN

2

Implement PoN code into Variant Calling

Gammerdinger

mistrm82

some great visualizations if we aggregate this data Maybe add an exercise to create it?

mistrm82

In snpEff it looks like there is a -cancerSamples option so that we don't need to use bcftools to add the pedigree line: -cancerSamples : Two column TXT file defining...

Gammerdinger