bcftools

all

Tools for manipulating VCF and BCF files.

Options (7)

-O, --output-typeboolean

View BCF file and convert to [v]CF on `stdout`

Example: bcftools view {{path/to/input.bcf}} {{[-O|--output-type]}} v

-o, --outputboolean

Sort a VCF file variants by chromosome and position, output to a [b]CF file, and index the sorted output

Example:

bcftools sort {{path/to/input.vcf.gz}} {{[-O|--output-type]}} b {{[-o|--output]}} {{path/to/sorted.bcf}} {{[-W|--write-index]}}

-W, --write-indexboolean

Sort a VCF file variants by chromosome and position, output to a [b]CF file, and index the sorted output

Example:

bcftools sort {{path/to/input.vcf.gz}} {{[-O|--output-type]}} b {{[-o|--output]}} {{path/to/sorted.bcf}} {{[-W|--write-index]}}

-e, --excludeboolean

Filter for low quality variants and annotate with "LowQual" tag in the FILTER column

Example: bcftools filter {{[-e|--exclude]}} 'QUAL<20' {{[-s|--soft-filter]}} LowQual {{path/to/input.vcf.gz}}

-s, --soft-filterboolean

Filter for low quality variants and annotate with "LowQual" tag in the FILTER column

Example: bcftools filter {{[-e|--exclude]}} 'QUAL<20' {{[-s|--soft-filter]}} LowQual {{path/to/input.vcf.gz}}

-a, --annotationsboolean

Add annotated columns from a tabix-indexed table on `stdout`

Example:

bcftools annotate {{[-a|--annotations]}} {{path/to/annotations.tsv.gz}} {{[-c|--columns]}} CHROM,POS,REF,ALT,INFO/AF {{path/to/input.vcf.gz}}

-c, --columnsboolean

Add annotated columns from a tabix-indexed table on `stdout`

Example:

bcftools annotate {{[-a|--annotations]}} {{path/to/annotations.tsv.gz}} {{[-c|--columns]}} CHROM,POS,REF,ALT,INFO/AF {{path/to/input.vcf.gz}}

View BCF file and convert to [v]CF on `stdout`

bcftools view path/to/input.bcf [-O|--output-type] v

Sort a VCF file variants by chromosome and position, output to a [b]CF file, and index the sorted output

bcftools sort path/to/input.vcf.gz [-O|--output-type] b [-o|--output] path/to/sorted.bcf [-W|--write-index]

Concatenate sorted VCF files that share the same samples to [z]ipped VCF on `stdout`

bcftools concat path/to/chr1.vcf.gz path/to/chr2.vcf.gz ... [-O|--output-type] z

Filter for low quality variants and annotate with "LowQual" tag in the FILTER column

bcftools filter [-e|--exclude] 'QUAL<20' [-s|--soft-filter] LowQual path/to/input.vcf.gz

Add annotated columns from a tabix-indexed table on `stdout`

bcftools annotate [-a|--annotations] path/to/annotations.tsv.gz [-c|--columns] CHROM,POS,REF,ALT,INFO/AF path/to/input.vcf.gz

Output variant [i]nter[sec]tion between VCF files using 4 threads

bcftools isec path/to/a.vcf.gz path/to/b.vcf.gz ... --threads 4 [-o|--output] path/to/intersection.vcf

Merge non-overlapping samples from VCF files without indices on `stdout`

bcftools merge path/to/cohort1.vcf.gz path/to/cohort2.vcf.gz --no-index

Create index for a bgzipped VCF file

bcftools index path/to/input.vcf.gz