Question about exon-seq data analysis for mutation detection.
I have some exon-seq data and DNA-Seq data from the same samples. The matched normal data is done in whole-genome. I want to compare the mutation detection between exon-Seq and whole-genome sequencing.
Step 1. It makes more sense to map exon-seq data to transcripts after removing introns. Step 2. When comparing with matched normal to call exon-seq mutation, I need to convert the alignement result on transcripts exon into whole genome coordinate because the matched normal alignment is done on whole-genome.
Questions: 1. Is there a pipeline that can do this conversion from transcript exon coordinates into whole-genome coordinates for aligned BAM/SAM file? 2. In general, what would be a better pipeline to call mutation from exon-seq data? or anyone can point me to some resource for this issue?
thanks in advance.