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apriha / snps

tools for reading, writing, merging, and remapping SNPs
BSD 3-Clause "New" or "Revised" License
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Identify and filter low quality SNPs #146

Closed apriha closed 1 year ago

apriha commented 2 years ago

Integrate @changlubio's GenomePrep capability to identify and filter low quality SNPs for a SNP array that are "not statistically plausible" based on analysis of 1000 Genomes Project data.

Requires resolution of #145.

Reference: C. Lu, B. Greshake Tzovaras, J. Gough, A survey of direct-to-consumer genotype data,and quality control tool (GenomePrep) for research, Computational and Structural Biotechnology Journal(2021), doi: https://doi.org/10.1016/j.csbj.2021.06.040

apriha commented 2 years ago

Resource available here: https://supfam.mrc-lmb.cam.ac.uk/GenomePrep/datadir/badalleles.tsv.gz