bcftools
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Bcftools Command: Output Variant Intersection Between Vcf Files
Use for output variant intersection between vcf files with Bcftools. Exact CLI syntax to output variant intersection between vcf files using Bcftools.
When to use this: Use for output variant intersection between vcf files with Bcftools.
Command Syntax
bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf>bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf>Command Breakdown
--threads- Command Option
- Tool-specific option used by this command invocation.
-o- Command Option
- Tool-specific option used by this command invocation.
FAQ
Purpose: Exact syntax to output variant intersection between vcf files 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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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>