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Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling.
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Based on SOC occupation classification
Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
Use when running GATK HaplotypeCaller to emit per-sample germline variant calls or gVCFs from analysis-ready BAM/CRAM inputs.
Use when splitting mixed accession-like text into one lowercase token per line in EDirect-style text pipelines.
Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.
Use when pretty-printing tab-delimited output with left, center, right, or decimal-aware numeric alignment in EDirect text workflows.
Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.
| name | bcftools |
| description | Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling. |
| disable-model-invocation | true |
| user-invocable | true |
bcftools/home/vimalinx/miniforge3/envs/bio/bin/bcftoolsview, norm, query, stats, call, or mpileup.# 1) Subset and view a compressed VCF
bcftools view -r chr1:100000-110000 cohort.vcf.gz
# 2) Normalize variants against a reference
bcftools norm -f reference.fa -Oz -o cohort.norm.vcf.gz cohort.vcf.gz
bcftools index cohort.norm.vcf.gz
# 3) Extract tabular fields
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT]\n' cohort.vcf.gz
# 4) Produce summary statistics
bcftools stats cohort.vcf.gz > cohort.stats.txt
view or filter to subset before heavier operations.norm before comparing or merging callsets.query and stats for reporting instead of ad hoc parsing when possible.bcftools norm needs the correct reference FASTA to do honest left-alignment and normalization.plugin -lv before reinventing functionality that already exists in a plugin.-Oz or BCF output with -Ob when building pipelines.