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Old 02-20-2019, 01:41 PM   #1
elmoremh
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Location: Cambridge, MA

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Default Programs for making diploid alternate references with phased variants

I want to make alternate references using phased variants. (Really I just want the sequences of two genes and the space between them, <10 kb). My individuals are diploid, which is why I needed to phase the variants.

However, the alternate reference programs I've found, like GATK AlternateReference, vcf2fasta, and bcftools, don't seem to take diploidy into account. They just stick in all variants and throw out one variant randomly if there are two at the same locus. And even if there was a program that did, these are not long, contiguous haplotypes so I can see how it would be difficult :\

Does anyone know of any solution to this? Anything better than imposing the variants manually? I guess I could do quick assemblies of only the reads mapped to my region but I'd be giving up the higher quality of my GATK-called variants.
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