Qtltools

• QTLtools-ase(1) Measure ASE from RNA-seq
• QTLtools-bamstat(1) Calculate stats of overlap between an RNAseq BAM file and an annotation
• QTLtools-cis(1) cis QTL analysis
• QTLtools-correct(1) Corrects genotypes or phenotypes with the provided covariates
• QTLtools-extract(1) Data extraction mode.
• QTLtools-fdensity(1) Functional density around molecular QTLs
• QTLtools-fenrich(1) Functional enrichment of molecular QTLs
• QTLtools-gwas(1) Genome-wide association tests
• QTLtools-mbv(1) Match genotypes in a VCF to a BAM file
• QTLtools-pca(1) Conducts PCA
• QTLtools-quan(1) Quantify gene and exon expression from RNA-seq
• QTLtools-rep(1) Replicate QTL associations in an independent dataset
• QTLtools-rtc-union(1) Find the union of QTLs from independent datasets
• QTLtools-rtc(1) Regulatory Trait Concordance score analysis
• QTLtools-trans(1) trans QTL analysis
• QTLtools(1) A complete tool set for molecular QTL discovery and analysis