Thanks, Chris! That was a helpful blog post. Is "indel normalization" the same thing as left alignment? And, when it comes down to biology, two records this like are indeed referring to the same variants, right?
~Sarah
-----Original Message-----
From: Oxford Statistical Genetics Software [mailto:[log in to unmask]] On Behalf Of Christopher Chang
Sent: Saturday, January 09, 2016 11:42 PM
To: [log in to unmask]
Subject: Re: [OXSTATGEN] 1000G ref data - same pos, alleles, reversed ref <> alt
The blog post at http://apol1.blogspot.com/2014/11/best-practice-for-converting-vcf-files.html includes an example of two variants which, after indel normalization, look identical except for swapped ref/alt order. This is rare, but it's a known possibility.
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