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is there a special way to encode homopolymer indels in vcf format?

Is there a special way to encode homopolymer indels in vcf format?

In vcf, indels are left-aligned, which means homopolymer indels will not be directly differentiated from other indels from the entry in vcf.

See for example this blogpost:

http://apol1.blogspot.co.uk/2014/05/how-do-i-identify-all-homopolymer-run.html

Is there an established procedure in vcf notation, to describe homopolymer indels in their full homopolymer length instead of left-aligned?

vcf
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updated by Ram Ram • written by 14134125465346445 14134125465346445

1 answer

You could symbolize a new ALT allele in the VCF header:

##ALT=<ID=Poly1,Description="My HomoPolymer Polymorphism 1">
##ALT=<ID=Poly2,Description="My HomoPolymer Polymorphism 2">

and use those Mutations in the VCF ?

chr1  12345  . A <Poly1>,<Poly2>   . . GT 1/1  2/2
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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