Installation
About
Standardize the pre-processing of genomic variants before performing a bacterial genome-wide association study (bGWAS). 'prewas' creates a variant matrix (where each row is a variant, each column is a sample, and the entries are presence - 1 - or absence - 0 - of the variant) that can be used as input for bGWAS tools. When creating the binary variant matrix, 'prewas' can perform 3 pre-processing steps including: dealing with multiallelic SNPs, (optional) dealing with SNPs in overlapping genes, and choosing a reference allele. 'prewas' can output matrices for use with both SNP-based bGWAS and gene-based bGWAS. This method is described in Saund et al. (2020) doi:10.1099/mgen.0.000368. 'prewas' can also provide gene matrices for variants with specific annotations from the 'SnpEff' software (Cingolani et al. 2012).
Citation | prewas citation info |
github.com/Snitkin-Lab-Umich/prewas | |
Bug report | File report |
Key Metrics
Downloads
Yesterday | 9 0% |
Last 7 days | 12 -20% |
Last 30 days | 62 -7% |
Last 90 days | 237 +32% |
Last 365 days | 781 -68% |