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Use when working with GATK MarkDuplicates, Picard MarkDuplicates through the GATK wrapper, duplicate marking in BAM or CRAM files, duplicate metrics, or optical duplicate detection in short-read DNA s
Use with AI
Install the MCP server or CLI to instantly fetch gatk-markduplicates documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gatk-markduplicates
Use when working with bigsnpr — an R package for analysis of massive
1 shared topic • 2 shared operations
Use when working with MIP (Medical Information Process) — a workflow management system for clinical whole-genome and whole-exome sequencing analysis. Runs end-to-end rare disease (rd_dna, rd_rna) and
1 shared topic • 2 shared operations
Peddy — pedigree and sample QC tool for VCF files. Verifies sample sex from X-chromosome heterozygosity, checks relatedness against PED file expectations, predicts ancestry via PCA against 1000 Genome
1 shared topic • 2 shared operations
Poseidon — a framework for organizing, sharing, and managing archaeogenetic genotype datasets. Standardized package format (POSEIDON.yml, .janno metadata, .ssf sequencing source files, .bib bibliograp
1 shared topic • 2 shared operations
REViewer — haplotype-resolved visualization of read alignments at short tandem repeat (STR) loci detected by ExpansionHunter. Accepts a sorted BAM/CRAM file, an ExpansionHunter VCF, a reference FASTA,
1 shared topic • 2 shared operations