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?
$\begingroup$
$\endgroup$
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? $\endgroup$– winni2kMay 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. $\endgroup$– burgerMay 13, 2021 at 2:50
Add a comment
|
1 Answer
$\begingroup$
$\endgroup$
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.
