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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
66 stars 9 forks source link

AAscore software #73

Closed nathanLauHKGI closed 10 months ago

nathanLauHKGI commented 10 months ago

Are there any existing software to get AAscore for a VCF file?

It is mentioned in the following paper: Statistical phasing of 150,119 sequenced genomes in the UK Biobank

Thank you

rwk-unil commented 10 months ago

The AAscore is given by GraphTyper GitHub : https://github.com/DecodeGenetics/graphtyper Refer to their manual : https://github.com/DecodeGenetics/graphtyper/wiki/User-guide#snp-and-indel-filtering

see" The sequences of 150,119 genomes in the UK Biobank" paper "SNP and Indels" section, link : https://www.nature.com/articles/s41586-022-04965-x#Sec2 it describes that the AAscore comes from GraphTyper for the 150,119 sequenced genomes in the UK Biobank.