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Are there any good options for calling variants or even just a pileup from R? R is not ideal for this, but I'd like to integrate with other functions.

I found deepSNV::bam2R which roughly does what I am looking for. Are there any alternatives?

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  • $\begingroup$ You can always call out to the shell from R. Do you need the solution to be pure R, or could it be a library hosted on CRAN, bioconductor, or even conda? How are you controlling your dependencies? $\endgroup$
    – winni2k
    May 11 at 12:18
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    $\begingroup$ @winni2k I was just looking for an R package. I am assuming the package is taking care of any dependencies. $\endgroup$
    – burger
    May 13 at 2:50
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Samtools/bcftools/tabix is available in R via Rsamtools.

SEQprocess also provides wrappers for different tools such as GATK and bowtie.

More utility packages are noted here.

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