Nco

BCFtools — comprehensive toolkit for manipulating variant calls in VCF and BCF format. Provides variant calling (mpileup + call), filtering, querying, merging, concatenation, normalization, annotation

1 shared topic • 2 shared operations

Limnology (freshwater science) — computational toolkit for freshwater ecosystem analysis including lake thermal stratification (rLakeAnalyzer), lake metabolism estimation (LakeMetabolizer), eDNA metab

1 shared topic • 2 shared operations

Use when performing GWAS fine-mapping with PAINTOR (Probabilistic Annotation INTegratOR). Computes posterior inclusion probabilities (PIPs) for causal variants by integrating summary statistics (Z-sco

1 shared topic • 2 shared operations

pairtools — Command-line toolkit for processing Hi-C and chromosome conformation capture contact pairs in the Open2C ecosystem. Parses alignments (SAM/BAM) into .pairs format, sorts, deduplicates, fil

1 shared topic • 2 shared operations

Use when working with PolyFun — functionally-informed polygenic fine-mapping from GWAS summary statistics. Computes per-SNP heritability priors using S-LDSC with functional annotations, then runs SuSi

1 shared topic • 2 shared operations