Search the literature for sensible QC options in Amplicon sequencing

[sanjaynagi]

• need to ensure we are implementing some sensible QC steps, I dont quite know what these would look like atm.

[ChabbyTMD]

Possible QC tool: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7

[sanjaynagi]

Suggestion from @eddUG to use qualimap on the BAM files, aswell as just the current samtools flagstat which is pretty basic.

[sanjaynagi]

Think this is pretty much resolved by #27 #26 . Now we just need QC for Variant calling. Will make a new issue.