1
$\begingroup$

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?

$\endgroup$
2
  • $\begingroup$ 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, 2021 at 12:18
  • 1
    $\begingroup$ @winni2k I was just looking for an R package. I am assuming the package is taking care of any dependencies. $\endgroup$
    – burger
    May 13, 2021 at 2:50

1 Answer 1

1
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.