Question: Haplotype frequency calculation from .vcf files
0
gravatar for daniel.castanedamogo
17 months ago by
daniel.castanedamogo0 wrote:

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!

sequencing snp • 622 views
ADD COMMENTlink modified 17 months ago by Vitis2.4k • written 17 months ago by daniel.castanedamogo0
3
gravatar for Vitis
17 months ago by
Vitis2.4k
New York
Vitis2.4k wrote:

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.

ADD COMMENTlink written 17 months ago by Vitis2.4k

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

ADD REPLYlink written 13 months ago by daniel.castanedamogo0
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