search

seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
74 stars 23 forks source link

Haplogroup Quality score >1？ #35

Open nanshanjin opened 4 years ago

nanshanjin commented 4 years ago
The table is result of my haplogrep2 Quality score and some quality score >1 ，Is this situation right？ Rank Quality Not_Found_Polys
1 0.8112 16217C
1 0.8674 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16180d 16181d 16360T
1 0.9935 514d 515d 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16183C 16360T 16519C
1 0.912 310.1C 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T
1 0.8964 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T
1 1.1261 827G 5093C 9329A 10398G 13269G 15535T 16129A 16180d 16181d
1 0.9181 827G 5093C 6302G 9329A 12654G 13269G 15535T 16129A 16360T 16519C
1 0.9626 827G 6302G 9329A 10398G 12654G 15535T 16180d 16181d 16261T 16360T
1 1.035 514d 515d 827G 5093C 6302G 9329A 10398G 12654G 13269G 15535T 16129A 16360T 16519C
1 1.1058 827G 6302G 9329A 10398G 12654G 15535T 16183C 16360T 16519C
stephenturner commented 4 years ago

FWIW, I've seen this a couple of times as well, running the CLI version.

seppinho commented 4 years ago

any chances that you can share the file? thanks!

seppinho commented 4 years ago

Would be fantastic if you can give the latest version a try. For FASTA, we excluded heteroplasmis sites from the input profile (resulted in score > 1) and adapted the range.

stephenturner commented 4 years ago

Thanks Sebastian! We were using a VCF file at the time. Unfortunately it's a sample that can't leave the building, but I'll see if we can test 2.2.6 on that sample.

seppinho commented 4 years ago

Thanks for the feedback, fyi the new version only fixes the FASTA related issues with the score. I'll look into the VCF problem, Hansi pointed out that this is related to insertions.