Is there precedent for and/or is it sensible to use DESeq or EdgeR to model counts of reads supporting variants in order to get significance?
For example, suppose I have 10 cases and 10 controls in a 20 sample VCF, can I extract the counts of alternate alleles (after filtering) into a counts matrix to these tools without violating their assumptions?
Some have recommended that I do a contingency table on number of cases / controls with / without the variant to get significance but that is discarding a lot of information.
thanks,
-Brent
EDIT: I suppose the difficulty is adjusting for depth at each site.
For example, suppose I have 10 cases and 10 controls in a 20 sample VCF, can I extract the counts of alternate alleles (after filtering) into a counts matrix to these tools without violating their assumptions?
Some have recommended that I do a contingency table on number of cases / controls with / without the variant to get significance but that is discarding a lot of information.
thanks,
-Brent
EDIT: I suppose the difficulty is adjusting for depth at each site.
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