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Bcftools Command: Sort Vcf

Use for sort vcf with Bcftools. Exact CLI syntax to sort vcf using Bcftools.

When to use this: Use for sort vcf with Bcftools.

Command Syntax

bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W

bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W

Command Breakdown

-O: Command Option; Tool-specific option used by this command invocation.
-o: Command Option; Tool-specific option used by this command invocation.
-W: Command Option; Tool-specific option used by this command invocation.

FAQ

Purpose: Exact syntax to sort vcf using Bcftools.

Test path: Replace placeholders and run destructive commands in a disposable workspace first.

Flag behavior: Tool version, platform, and shell can change behavior.

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Suggest a correction, safer default, or version-specific note for this entry.

Related Operations

Bcftools Command: View Bcf bcftools view <path/to/input.bcf> -O v Bcftools Command: Concat Vcf bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z Bcftools Command: Filter Variants bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz> 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 Command: Intersection Vcf bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf>

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