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6.5 years ago
fabbri.marco
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10
I was asked to reanalyse exome data (illumina DNA) I am interested only to 50 genes. Can I limit the allignement to the genes of interest ? Since the samples are 400, I would like to save time. Thanks Marco
See: Is There Any Reference Exome ?
The short answer to your question is 'no'. You can use regions for mutation calling to reduce to your 50 genes though (e.g. the -L flag if calling mutations with GATK)
Without going into a long explanation, I tend to agree with Bruce here. I think that you should just do the alignment over the entire genome and then filter down on your regions of interest (your 50 genes) with a BED file.
Look at it this way: if you tried to publish this work and any reasonably skilled analyst saw the methods, they'd criticise you for just aligning to just your 50 genes of interest (and you would have to re-do everything).