CmdID

CmdID / Commands

bcftools

Tools for manipulating VCF and BCF files. tldr-pages

On several platforms

Opens CmdID with your command. It is read in your browser and sent nowhere.

Several platforms

from tldr-pages, CC BY 4.0

View BCF file and convert to vCF on stdout

bcftools view path/to/input.bcf --output-type vIdentify

Sort a VCF file variants by chromosome and position, output to a bCF file, and index the sorted output

bcftools sort path/to/input.vcf.gz --output-type b --output path/to/sorted.bcf --write-indexIdentify

Concatenate sorted VCF files that share the same samples to zipped VCF on stdout

bcftools concat path/to/chr1.vcf.gz path/to/chr2.vcf.gz ... --output-type zIdentify

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

bcftools filter --exclude 'QUAL<20' --soft-filter LowQual path/to/input.vcf.gzIdentify

Add annotated columns from a tabix-indexed table on stdout

bcftools annotate --annotations path/to/annotations.tsv.gz --columns CHROM,POS,REF,ALT,INFO/AF path/to/input.vcf.gzIdentify

Output variant intersection between VCF files using 4 threads

bcftools isec path/to/a.vcf.gz path/to/b.vcf.gz ... --threads 4 --output path/to/intersection.vcfIdentify

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

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

Create index for a bgzipped VCF file

bcftools index path/to/input.vcf.gzIdentify