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compareSTR length genotype assumption #154

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hopedisastro opened this issue Mar 7, 2022 · 0 comments
Open

compareSTR length genotype assumption #154

hopedisastro opened this issue Mar 7, 2022 · 0 comments

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@hopedisastro
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hopedisastro commented Mar 7, 2022 •
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Hi,
I'm trying to compare STR calls from GangSTR and ExpansionHunter using compareSTR. compareSTR was able to run and provide output files but I received the warning below. Why does this warning occur and how can I explicitly request length based genotypes?

tr_harmonizer.py:928: UserWarning: String genotypes have been requested for a TRRecord generated by a caller which only generates length genotypes, not string genotypes. Returning a fabricated string genotype. Consider requesting length based genotypes instead.
warnings.warn("String genotypes have been requested for a"
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@hopedisastro