snps icon indicating copy to clipboard operation
snps copied to clipboard

Identify and filter low quality SNPs

Open apriha opened this issue 3 years ago • 1 comments

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 avatar Oct 18 '21 03:10 apriha

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

apriha avatar Oct 20 '21 04:10 apriha