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genepi / haplogrep3

Free mtDNA Haplogroup Classification Service
https://haplogrep.i-med.ac.at/
MIT License
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Quality Formula Not Defined #33

Closed DarioS closed 1 year ago

DarioS commented 1 year ago

The output has Quality column but how this is calculated doesn't appear to be defined anywhere. What is the mathemtical formula?

$ cat testOutput.txt 
"SampleID"      "Haplogroup"    "Rank"  "Quality"       "Range"
"7_21_11450"    "H"     "1"     "0.7604"        "1-16569"
"7_21_11555"    "H2a2a1"        "1"     "0.5000"        "1-16569"
"7_21_11556"    "H"     "1"     "0.7604"        "1-16569"
"7_21_11557"    "H2"    "1"     "0.8025"        "1-16569"
"7_21_11576"    "H2a"   "1"     "0.7423"        "1-16569"
"7_21_14555"    "H"     "1"     "0.9236"        "1-16569"
"7_21_14557"    "H"     "1"     "0.9236"        "1-16569"
"7_21_KOLF21"   "H"     "1"     "0.7604"        "1-16569"
"7_21_RM35"     "H2a2a" "1"     "1.0000"        "1-16569"

Some guidance for interpreting Quality should be provided in the documentation. What is the numeric range? What are bad values?

seppinho commented 1 year ago

Hi, see docs: https://haplogrep.readthedocs.io/en/latest/kulczynski/. The formula is also defined in the init paper: https://onlinelibrary.wiley.com/doi/full/10.1002/humu.21382

best. sebastian