WGS of Plasmodium falciparum 3D7: control, rep 1, timepoint 2
To call variants (SNPs/indels) in the transfected lines compared to a previously sequenced control 3D7 line, genomic DNA reads were first trimmed to adapters and aligned to the Homo sapiens genome (assembly GRCh38) to remove human-mapped reads. Remaining reads were aligned to the P. falciparum 3D7 genome using bwa (version 0.7.17) and PCR duplicates were removed using PicardTools (Broad Institute). GATK HaplotypeCaller (https://gatk.broadinstitute.org/hc/en-us) was used to call variants between the sample and the 3D7 reference genome for both the transfected lines and the 3D7 control.