An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis

Malaria Journal

Table 1 Resistant k13 mutations detected by the optimized GATK4 at hexaploid and diploid modes versus GATK3

K13 mutations	Optimized GATK4 (ploidy6)	Optimized GATK4 (ploidy2)	GATK3
A481V	5	5	5
C580Y	664	649	650
G449A	6	5	5
G538V	24	21	21
I543T	36	34	33
M446I	38	36	36
N458Y	17	17	17
P441L	28	28	28
P553L	24	23	23
P574L	30	30	30
R539T	65	63	62
R561H	24	24	24
Y493H	111	106	106

All the mutations were found in South-East Asia except for one sample carrying the C580Y allele that was collected in Cameroon

ISSN: 1475-2875