PHG rankingFile mandatory when haplotypes not from assemblies?
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7 weeks ago
dovi ▴ 60

Hi everyone,

for the PHG version >1.0 the rankingFile (when creating consensus) is mandatory. However the description of the RankingFile is:

rankingFile - path to a ranking file. If your haplotypes were created from Assemblies, you need to produce a method ranking the taxon. This file will take the form: taxon\tscore where higher scores mean we trust that taxon more highly. Do not include a header line. When clustering assemblies, when we have a cluster of similar haplotypes, we choose whichever taxon in that group which has the higher ranking score. To break ties, be sure to give each taxon a different score. One simple way to score things is to count the number of haplotypes covered by each taxon in the DB and use that count as the score. Any other arbitrary ranking can be used.

rankingFile is required when clusteringMode is upgma_assembly or kmer_assembly, and not for method "upgma". However according to the documentation, method "upgma" is no longer supported in PHG version 1.0, so I only have two options left, and both require the rankingFile.

I wonder if then the two clusteringMethods are only meant for haplotypes from Assemblies and there is no longer method for haplotypes from WGS in version >1.0. And in the case that clusteringMethods are also meant for haplotypes from WGS, why do I have to provide the rankingFile?

Thanks!

PHG • 87 views
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