Question: Splice prediction from bam files
0
gravatar for vigprasud
3.0 years ago by
vigprasud60
United States
vigprasud60 wrote:

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

wes splicesite • 963 views
ADD COMMENTlink modified 3.0 years ago by WouterDeCoster42k • written 3.0 years ago by vigprasud60

From DNA-Seq, or RNA-Seq?

ADD REPLYlink written 3.0 years ago by d-cameron2.1k

DNA-seq bams

ADD REPLYlink written 3.0 years ago by vigprasud60
1
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster42k wrote:

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.

ADD COMMENTlink written 3.0 years ago by WouterDeCoster42k
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