bcftools-variant-manipulation
De la autor
CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
Instalare
npx skills add jaechang-hits/SciAgent-Skills --skill bcftools-variant-manipulation -a claude-code
Se instalează în .claude/skills/bcftools-variant-manipulation/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
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De ce 86
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- vcf-variant-filteringjaechang-hits/SciAgent-SkillsGuide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.Productivitate★ 382
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- tiledbvcfK-Dense-AI/scientific-agent-skillsStores and retrieves genomic variant calls with TileDB-VCF. Use for indexed single-sample VCF/BCF ingestion, incremental cohorts, region and sample queries, streaming results, allele statistics, QC, and VCF/BCF export locally or through TileDB Cloud.Știință★ 54.1K
- snpeff-variant-annotationjaechang-hits/SciAgent-SkillsAnnotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl VEP for REST API; SnpEff for fast CLI with pre-built genomes.Date★ 382
- bedtools-genomic-intervalsjaechang-hits/SciAgent-SkillsGenomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.Știință★ 382
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