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BEAGLE for genotype phasing and imputation from VCF files. Performs haplotype phase inference for genotyped variants, imputes ungenotyped markers using a reference panel, and estimates identity-by-des
Use with AI
Install the MCP server or CLI to instantly fetch BEAGLE documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/beagle
CNVnator — read-depth (RD) based copy number variation (CNV) detection from whole-genome sequencing BAM/CRAM files. Partitions the genome into equal-size bins, computes normalized read-depth signals,
3 shared topics • 1 shared operation
CNVpytor — Python tool for copy number variation (CNV) detection from whole-genome sequencing (WGS) BAM/CRAM files. Analyzes read depth signals with adjustable bin sizes, calls deletions and duplicati
3 shared topics • 1 shared operation
Use when working with sQTLseekeR — splicing quantitative trait locus (sQTL) mapping using transcript ratio tests. R package that identifies genetic variants (SNPs, indels) associated with changes in s
3 shared topics • 1 shared operation
vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,
3 shared topics • 1 shared operation
NgsRelate — pairwise relatedness estimation from NGS data using genotype likelihoods. Estimates kinship coefficients, R0/R1/KING-robust statistics, and inbreeding coefficients from VCF/BCF files or AN
3 shared topics