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Bcftools Commands
23 bcftools entries
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bcftools Archive
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 Archive
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 Archive
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 Archive
Bcftools Command: Concat Vcf
bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z bcftools Archive
Bcftools Command: Concatenate Sorted Vcf Files
bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z bcftools Archive
Bcftools Command: Concatenate Sorted Vcf Files To Zipped Vcf
bcftools concat <path/to/chr1.vcf.gz path/to/chr2.vcf.gz ...> -O z bcftools Archive
Bcftools Command: Create Index For Bgzipped Vcf
bcftools index <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Create Index For Bgzipped Vcf File
bcftools index <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Filter Low Quality Variants
bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Filter Low Quality Variants And Annotate
bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Filter Variants
bcftools filter -e 'QUAL<20' -s LowQual <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Index Vcf
bcftools index <path/to/input.vcf.gz> bcftools Archive
Bcftools Command: Intersection Vcf
bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf> bcftools Archive
Bcftools Command: Merge Non Overlapping Samples From Vcf
bcftools merge <path/to/cohort1.vcf.gz> <path/to/cohort2.vcf.gz> --no-index bcftools Archive
Bcftools Command: Merge Non Overlapping Samples From Vcf Files
bcftools merge <path/to/cohort1.vcf.gz> <path/to/cohort2.vcf.gz> --no-index bcftools Archive
Bcftools Command: Merge Vcf
bcftools merge <path/to/cohort1.vcf.gz> <path/to/cohort2.vcf.gz> --no-index bcftools Archive
Bcftools Command: Output Variant Intersection Between Vcf Files
bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf> bcftools Archive
Bcftools Command: Output Variant Intersection Using Threads
bcftools isec <path/to/a.vcf.gz path/to/b.vcf.gz ...> --threads 4 -o <path/to/intersection.vcf> bcftools Archive
Bcftools Command: Sort Vcf
bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W bcftools Archive
Bcftools Command: Sort Vcf File And Index Output
bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W bcftools Archive
Bcftools Command: Sort Vcf File Variants
bcftools sort <path/to/input.vcf.gz> -O b -o <path/to/sorted.bcf> -W bcftools Operations
Bcftools Command: View Bcf
bcftools view <path/to/input.bcf> -O v bcftools Operations
Bcftools Command: View Bcf File And Convert To Vcf
bcftools view <path/to/input.bcf> -O v