Imputation #188
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How does PHG_v2 handle the imputation of a sample if one or few of its ancestral genomes are not included in the pangenome itself? Does it still attempt to impute the 'most likely path' or it does not impute that region of the genome? |
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Hello, If a sample has ancestral genomes that are not included in the pangenome the PHGv2 by default will attempt to impute the regions which it does not have read support for. You can set --min-reads to 1 or higher to prevent this during the find-paths step. But you will likely have gaps(reference ranges where a Haplotype is not called) in the path wherever you have reference ranges which do not have a single read hitting a Haplotype within that range. |
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Okay, thank you for the quick response! |
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Hello,
If a sample has ancestral genomes that are not included in the pangenome the PHGv2 by default will attempt to impute the regions which it does not have read support for.
You can set --min-reads to 1 or higher to prevent this during the find-paths step. But you will likely have gaps(reference ranges where a Haplotype is not called) in the path wherever you have reference ranges which do not have a single read hitting a Haplotype within that range.