A (n initially) pooled GWAS study of piperiquine resistance in P. falciparum isolates from Cambodia. About 40 low IC50 and 20 high IC50 samples were pooled then prepped and run on one MiSeq 2x250 run. Please see the project wiki for more details.
- Alignment (BWA-MEM or BT2?)
- Deduplication (GATK)
- Realignment (GATK)
- GWAS Analysis by Popoolation2