bcftools
Verified for current stable LTS
Bcftools Commands
Bcftools command syntax with verified terminal examples.
Commands
8 commands for Bcftools
bcftools Operations
Bcftools Command: View Bcf
bcftools view <path/to/input.bcf> -O v bcftools Archive
Bcftools Command: Sort Vcf
bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W bcftools Archive
Bcftools Command: Concat Vcf
bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z bcftools Archive
Bcftools Command: Filter Variants
bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Annotate Vcf
bcftools annotate -a <path/to/annotations.tsv.gz> -c CHROM,POS,REF,ALT,INFO/AF <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Intersection Vcf
bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf> bcftools Archive
Bcftools Command: Merge Vcf
bcftools merge <path/to/cohort1.vcf.gz> <path/to/cohort2.vcf.gz> --no-index bcftools Archive
Bcftools Command: Index Vcf
bcftools index <path/to/input.vcf.gz> Suggest a Bcftools Command
Submit missing workflows, corrections, or verified alternatives for this tool.
FAQ
Coverage: Focused examples for common Bcftools workflows.
Verified version: current stable LTS.
Verification: Test commands in a disposable workspace and submit notes for edge cases.