bcftools
Verified for current stable LTS
Bcftools Command: Filter Low Quality Variants
Use for filter low quality variants with Bcftools. Exact CLI syntax to filter low quality variants using Bcftools.
When to use this: Use for filter low quality variants with Bcftools.
Command Syntax
bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz>bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz>Command Breakdown
-e- Command Option
- Tool-specific option used by this command invocation.
-s- Command Option
- Tool-specific option used by this command invocation.
FAQ
Purpose: Exact syntax to filter low quality variants 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: Add Annotated Columns From 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 bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z