Hi! I'm relatively new to bioinformatics and I've been working on haplotyping malaria based on the sequencing of two gene markers (msp1 and msp2). However, I have not found a good software/pipeline that can help me to calculate the haplotype frequency per sample (I've got 20 samples in total). I already have .vcf files after I compared against a reference genome for malaria (Plasmodium falciparum 3D7), but I am stuck in regards of how to calculate haplotypes and its frequency.
Thanks a lot!