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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!

snp sequencing
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updated by Azera22 • Azera22 • written by daniel.castanedamogo • daniel.castanedamogo

1 answer

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.

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written by Vitis Vitis

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!

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written by Azera22 • Azera22

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