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Tajima's D calculation for specific genes in multi-sample VCF

Hi, I have my data in vcf called using GATK's short variant discovery pipeline. Data is for 398 genes and sample size is 401. This is a targeted sequencing data not WGS one. I want to calculate tajima's D for each gene. I know vcftools can calculate Tajima's D in bins but due to varying length and gaps within genes it can't be applied here. Pegas and popgenome packages in R also calculate tajima's D either for entire dataset or in bins. How can I calculate Tajima's D for each gene separately?

neutrality genetics tajimad
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updated by xoaib • xoaib • written by Muhammad • Muhammad

1 answer

You can use this tool called vcf2tajima https://github.com/xoaib4/vcf2tajima

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written by xoaib • xoaib

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