Haplotype frequency calculation from .vcf files

Haplotype frequency calculation from .vcf files


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.

Any suggestions?

Thanks a lot!




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