how should one treat samples in sequencing
I have 2 control and 2 tumor samples which I have their exome sequencing data. I want to know if you should combine them after alignment during annotation or after annotation or when would be the best time to combine them ?
Or should I treat them separately ?
My other question is which database is best for mutation annotation?
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Are the samples from different individuals or are they matched tumor/normals?
Rather than database you would want to use
snpEfforVEPfrom Ensembl to do annotations.@genomax Can you tell me what should I do in both cases? do you have any idea how to download those databases? is there any differences between all these annotation tools?