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Haplotype caller, multisample calling on set of 9 solid and 1 ilumina sample

WimSWimS Posts: 25Member

How does the haplotype caller handle multiple samples? Does it do a local denovo assembly for every sample and then compare those or does it do 1 local denovo assembly using the reads of all the samples?

Can I run the haplotype caller on a set of 9 solid (50bp fragment and 50 x 35 PE) together with 1 ilumina sample (100 x 100 PE) ?

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