NGS DNA-seq analysis packages for mapping, calling cariants, annotation on R / bioconductor

Question

[houkto]

Hi,

I am looking for a complete DNA-seq analysis in R this including reads mapping, variants calling and annotation?

So far I found RNA-seq and Chip-seq packages only?

I would be grateful if you can points me to DNA-seq packages to analyse whole exome or targeted genes data (fastq) in R and preferable work through tutorial if exists?

Thanks

[Devon Ryan]

I really can't recommend using R for alignment and variant calling. R is best at data analysis, not batch processing of large datasets. That's why very few people try to do their whole pipeline in R and rather use R at the end.

BTW, for alignment you could use Rsubread.

[houkto]

Thanks, for the info. I did realise the issue with big data and R. Nevertheless, using Linux OS (whether fresh install or as virtual image) is not practical when it comes to demonstrate to colleges how basic DNA-seq analysis works especially in old machines.

Answer 1

[Sean Davis]

Targeted sequencing or exome sequence alignment and variant calling is best done using non-R-based tools (at least right now). One can use R to call system programs such as BWA and the GATK tools to do analysis up to VCF files. At that point, the VariantAnnotation package becomes quite useful for QC, annotation, filtering, and visualization of results.