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Yes, you seem to be right as far as GATK is concerned. Are there any other papers/software that implement some kind of normalization? -
Normalization by the library size during variant detection
Hello:
Suppose I have two libraries that do not have the same number of reads, but otherwise they are similar. During variant detection, more variants will be called in the larger library just because of the larger library size.
Are there any papers or software that perform normalization to adjust for the library size during variant detection? Unless I am mistaken, there is no normalization step in GATK pipeline. Please provide references if you can.
Thanks,
Nik
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