VCF file analysis
I have a VCF file and have few queries to solves. Can someone help me to proceed with the same?
The questions are as following:
- How many variant records does the file contain?
- How many genotype calls are there per variant record?
- Are the genotype calls phased or unphased?
- Write code or pseudo code (in any language of your choosing) to calculate allele frequencies for each variant in the file
- Design a relational database schema to store the following information: ● variant ID ● chromosomal location of the variant ● the alleles and their corresponding frequencies
- Write code or pseudo code to populate your database schema from the VCF file
- How might you store the genotypes such that they could be retrieved quickly, for a project that has produced genotypes for ~1200 individuals across ~80 million sites?
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Nyksubuz •
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Is this an assignment question? It sounds like it is. You need to show effort on your part if you hope to get any assistance.
I know nothing about vcf file analysis, so Im asking from where I can start atleast?
You should be able to search and find information about points you mentioned above easily. I will provide a few links to get you started.
VCF file format : https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format
Algorithms: https://gatk.broadinstitute.org/hc/en-us/sections/360007226771-Algorithms
Workflows: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
ok thank you, I will go through those
Look at the official VCF specification too. get your google fu out
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