genotyping or variant calling in R 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?
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.