6/7/2021: Tools for analyzing list of SNPs (mapping to genes, checking for enrichment, rank by given metric, etc.)
- SNPsToBed.R : takes a list of SNPs (either RSID or chr:pos) and converts into a bed file. If provide a list of values associated with the SNPs (scores, GWAS sum stats, etc.) can also return a list with just a certain percentage of the SNPs. Initially optimized for use with
gwas_decomp_ldsc, but moved here for wider use.
Rscript src/SNPsToBed.R --mapping gwas_extracts/seed2_thresh0.9_h2-0.1_vars1e-5/seed2_thresh0.9_h2-0.1_vars1e-5.pruned_rsids.txt \
--snp_list results/seed2_thresh0.9_h2-0.1_vars1e-5/factorization/snp.ids.txt \
--outdir results/seed2_thresh0.9_h2-0.1_vars1e-5/gene_set_enrichment/full_list.bed
- SNPsToTSV.R : takes a list of SNPs and (either RSID or chr:pos) and converts to a TSV file for querying on OpenCravat
- SNPsToGenes.sh : takes a BED file of SNPs and matches them to their closest genes. (hg19)