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Revision as of 21:58, 15 June 2014
, 21:58, 15 June 2014→Normalization
==Normalization==
==Normalization==
A slight digression here, when analyzing indels, it is important to normalize it. While it is a simple concept,
it is hardly standardized. The call set here had already been normalized but we feel that this is an important
concept so we discuss this a bit here.
Indel representation is not unique, you should normalize them and remove duplicates.
Indel representation is not unique, you should normalize them and remove duplicates.
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vt normalize mills.genotypes.bcf -r ~/ref/vt/grch37/hs37d5.fa -o + | vt mergedups + -o mills.normalized.genotypes.bcf
UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO.
==to document==
==to document==
