Haplotype frequency calculation from .vcf files

Question

[daniel.castanedamogo]

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!

Answer 1

[Vitis]

Haplotypes come from phased genotypes. First you need to phase the variants with tools like whatshap:

https://whatshap.readthedocs.io/en/latest/

Then you may use tools like plink to calculate haplotype frequencies.

[daniel.castanedamogo]

Thanks a lot! I'll give it a try!

[Azera22]

Hi, I know this is an old post, but I am trying to do a similar thing. I tried whatshap, but I think it is meant for diploid organisms, not haploid like Plasmodium. What did you end up using to solve this? Thanks!