JUelich NeuroImaging FEature extractoR
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hipsnp
<<< This is a development version, there is no any warranty that it works >>>
functions to handle SNP data, especially from the UKB.
>>> import hipsnp
>>> genotypes = hipsnp.vcf2genotype('snp_epilepsy.vcf')
>>> genotypes
sub-01 sub-02 sub-03 ... sub-04 sub-05 sub-06
rs1231232,6:12364007_T_T TT TT AC ... TC AC TT
rs1231231,6:12331231_C_A CA AC CC ... CC CC CA
[2 rows x 487409 columns]
resources
SNP databases
https://www.ncbi.nlm.nih.gov/snp/
http://www.ensembl.org/Homo_sapiens
Tools
https://www.well.ox.ac.uk/~gav/qctool/
Info
https://eu.idtdna.com/pages/education/decoded/article/genotyping-terms-to-know
https://faculty.washington.edu/browning/intro-to-vcf.html
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