GenoTools
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dvitale199
GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for...
**Is your feature request related to a problem? Please describe.** when running --ld with
**Describe the bug** gwas fails when trying to run with a phenotype that's not PHENO1 **To Reproduce** attempt to run gwas with a column that is anything but PHENO1 **Expected...
Currently, --covars and --pca used together results in defaulting to covars. we want to be able to run --pca and concat the pcs with the existing covars **Describe the solution...
**Is your feature request related to a problem? Please describe.** Need plotting method for summary statistics **Describe the solution you'd like** A clean, interactive manhattan plot implemented in plotly. zooming,...
**Describe the bug** when attempting to run containerized predictions, a user with an unknown OS encountered the following error: ``` Getting Common SNPs /usr/local/lib/python3.10/dist-packages/genotools/utils.py:404: DtypeWarning: Columns (0) have mixed types....
**Is your feature request related to a problem? Please describe.** currently have a separate reference panel labels file. labels should add these directly to the reference genotypes
we would like to output eigenvalues and create a scree plot
**Is your feature request related to a problem? Please describe.** Automated liftover between hg19/hg38 given a list of positions **Describe the solution you'd like** Store liftover and chain files in...
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GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for...