Splice prediction from bam files

Question

[vigprasud]

Are there any command line tools that specialize in predicting splice site variants from bams?

[d-cameron]

From DNA-Seq, or RNA-Seq?

[vigprasud]

DNA-seq bams

Answer 1

[WouterDeCoster]

You would first have to do variant calling, e.g. using GATK HaploTypeCaller. Then you need to annotate the obtained variants, e.g. using snpEff, VEP or Annovar to discover the expected consequence of a variant.

I'm not aware of a more specific tool, but knowing the myriad of tools available it probably does exist.