bcftools
Verified for current stable LTS
Bcftools Command: Filter Low Quality Variants And Annotate
Use for filter low quality variants and annotate with Bcftools. Exact CLI syntax to filter low quality variants and annotate using Bcftools.
When to use this: Use for filter low quality variants and annotate 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 and annotate 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