convert dartr to vcf keeping invariant sites to calculate nucleotide diversity (pi)
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Jéssica Fernanda
Aug 2, 2023, 9:17:09 AM8/2/23
to dartR
Hello all! :)
I have a DArTseq dataset of sardines for which I'm trying to calculate nucleotide diversity (pi) using either pixy or vcftools, as they consider invariant sites in the calculation (the recommended procedure; https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12635). However, I'm not being able to convert my dartr object to vcf including invariant sites in the dataset - apparently, only SNPs are exported. The only filters I apply to my dartr object are call rate, reproducibility and Hamming distance, in this order.
Does anyone know how to convert from dartr to vcf keeping invariant sites in the dataset so it is adequate for pi calculations?
I'm using dartR version 2.9.7 and R version 4.2.3 (but I've tried with different versions of R and dartR also using a genlight object, and with different filtering).
Kind regards,
I have a DArTseq dataset of sardines for which I'm trying to calculate nucleotide diversity (pi) using either pixy or vcftools, as they consider invariant sites in the calculation (the recommended procedure; https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12635). However, I'm not being able to convert my dartr object to vcf including invariant sites in the dataset - apparently, only SNPs are exported. The only filters I apply to my dartr object are call rate, reproducibility and Hamming distance, in this order.
Does anyone know how to convert from dartr to vcf keeping invariant sites in the dataset so it is adequate for pi calculations?
I'm using dartR version 2.9.7 and R version 4.2.3 (but I've tried with different versions of R and dartR also using a genlight object, and with different filtering).
Kind regards,
Jéss
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