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malariagen / ag1000g-phase1-vgsc-report

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Haplotype group assignment issue re F3/F4 #170

Closed alimanfoo closed 6 years ago

alimanfoo commented 6 years ago

In the original clustering analysis in the Ag1000G phase 1 paper, the variants D466H and I1940T are found in group F3 and not in F4:

image

This is concordant with the network analysis:

image

(Albeit these variants are no longer fixed in F3 but still at high frequency, so allowing some minor difference in group assignment.)

However in the supplementary table of tracking variants these are at high frequency in F4 and not F3.

alimanfoo commented 6 years ago

cc @ericrlucas, @cclarkson

alimanfoo commented 6 years ago

@EricRLucas just to say the issue with F3 and F4 has been resolved, they had got swapped in the supplementary data and some of the figures. Everything in the master branch should be fixed now and consistent with the phase 1 paper. Contact @cclarkson if any follow-up questions. Thanks again for picking this up.