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gatk-variant-calling

GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow. BAM files should be prepro...

by FreedomIntelligence

github 4 files

joint-calling

Call variants jointly across multiple samples for improved accuracy and consistent genotyping. Improved sensitivity - Leverage information across samp...

by FreedomIntelligence

github 3 files

variant-annotation

| Tool | Best For | Speed | Output | |------|----------|-------|--------| | bcftools csq | Simple consequence prediction | Fast | VCF | | VEP | Compre...

by FreedomIntelligence

github 3 files

variant-calling

Call SNPs and indels from aligned reads using bcftools. BAM file + Reference FASTA bcftools mpileup (generate pileup) bcftools call (call variants) VC...

by FreedomIntelligence

github 3 files

vcf-basics

View and query variant files using bcftools and cyvcf2. | Format | Description | Use Case | |--------|-------------|----------| | VCF | Text format, h...

by FreedomIntelligence

github 3 files

vcf-statistics

Generate statistics and quality metrics using bcftools. | Command | Purpose | |---------|---------| | bcftools stats | Comprehensive variant statistic...

by FreedomIntelligence

github 3 files

bio-microbiome-functional-prediction

Reference examples tested with: Biostrings 2.70+, ggplot2 3.5+, pandas 2.2+, phyloseq 1.46+, scanpy 1.10+ Before using code patterns, verify installed...

by FreedomIntelligence

github 3 files

bio-workflow-management-nextflow-pipelines

// main.nf nextflow.enable.dsl=2 params.reads = "data/{1,2}.fq.gz" params.outdir = "results" process FASTQC { input: tuple val(sampleid), path(reads) ...

by FreedomIntelligence

github 3 files

gene-database

NCBI Gene is a comprehensive database integrating gene information from diverse species. It provides nomenclature, reference sequences (RefSeqs), chro...

by FreedomIntelligence

github 6 files

bio-genome-engineering-prime-editing-design

Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pac...

by FreedomIntelligence

github 3 files

bio-epidemiological-genomics-variant-surveillance

Reference examples tested with: Nextclade 3.3+, ggplot2 3.5+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions dif...

by FreedomIntelligence

github 3 files

bio-pdb-geometric-analysis

Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: Python: ...

by FreedomIntelligence

github 5 files