freeseek
R wrapper of BCFTools score
Hi,
Thank you again for this great set of tools !
In the interest of promoting the adoption of gwas-vcf and my first time experience with your plugins (very fast !!), i made a package to bundle the plugin functions to be distributed in a R package https://sounkou-bioinfo.r-universe.dev/RBCFLib.
I made some minor change to make the bundling possible using an approach similar to the pysam strategy. As of now this provide a wrapper to bcftools and score, but the goal is to facilitate BCF centric classes for gwas data i/o in a more idiomatic R ways (data frame like objects)
I though this might be of interest to some R users of the tools and may be worth mentioning in the readme.
Best wishes !
Thank you @sounkou-bioinfo and I am glad the tools are useful to you. In the past I have often used a combination of bcftools query to output tables from VCFs and data.table::fread() to quickly load them into a data frame structure in R but clearly your tools go way beyond that
i might still do the data.table::fread() for the data loading bit if the other strategies (ALTREP, memory map files, delay arrays, etc) i am trying out don't pan out or would be much more involved than the scope of this package Thank you again