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Old 08-18-2016, 10:26 PM   #1
Location: Antwerp, Belgium

Join Date: Jan 2011
Posts: 14
Default allele order in phased VCF

Hi all,

I know related issues have been discussed before, but I can't find an answer to this specific question:

if you have a phased VCF file, how do the AD fields relate?

would you for example by phasing this:

GT:AD 0/1:42,35

go to

GT:AD 1|0:35,42

or do these fields (and PL fiels for example) keep there order related to the order of alleles listed under REF and ALT columns?
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