Dear All, We have whole exome sequencing data of ten samples from illumina. While I was looking for a pipeline to analyse this data i found a nice thread http://biostar.stackexchange.com/questions/1269/what-is-the-best-pipeline-for-human-whole-exome-sequencing
But, I am little bit confused in using this pipeline for all 10 samples together.
Should I first align each file to the genome independently,combine as single bam file and proceed further.?
or should I need to process every file independently through all these steps? If so what should I do finally to understand the result out of all 10 samples?