9.2 R Bioinformatics Toolkit
The R bioinformatics Toolkit app comes with a slew of useful packages preinstalled:
- bcftools (v1.9)
- bedtools (v2.29.0)
- bgzip (v1.9)
- plink (v1.90b6)
- sambamba (v0.7.0)
- samtools (v1.9)
- seqtk (v1.3 r106)
- tabix (v1.9)
- vcflib binaries (git revision 8bc93d8a74735b0fe6303f78b2764d6987ba1cde)
- GATK 4.0.2.1
- FreeBayes
- vArmyKnife
- picard tools
- R 3.6.1
- Every R package I’ve ever used + a bunch I’ve only heard about