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Bcftools Command: Sort Vcf File And Index Output

Use for sort vcf file and index output with Bcftools. Exact CLI syntax to sort vcf file and index output using Bcftools.

When to use this: Use for sort vcf file and index output 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 file and index output 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: Add Annotated Columns From Tabix Indexed Table bcftools annotate -a <path/to/annotations.tsv.gz> -c CHROM,POS,REF,ALT,INFO/AF <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: Concat Vcf bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z Bcftools Command: Concatenate Sorted Vcf Files To Zipped Vcf bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z Bcftools Command: Create Index For Bgzipped Vcf File bcftools index <path/to/input.vcf.gz>

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