Plugins

Important
In order to use the BCFtools plugins, this environment variable must be set and point to the correct location:
export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
If a plugin still does not work, bcftools +name -vv explains why it would not load.

For developers

Please read here.

List of plugins

ad-bias

Finds positions with ALT allele frequency significantly different between two samples. Performs a Fisher test on the FORMAT/AD annotation.

af-dist

Collects AF deviation stats and GT probability distribution given AF and assuming HWE

check-ploidy

Checks if ploidy of samples is consistent for all sites.

check-sparsity

Prints samples without genotypes in a region (-r/-R) or chromosome (the default)

color-chrs

Colors shared chromosomal segments shared. Requires phased GTs.

contrast

Finds novel alleles and genotypes in two groups of samples. Adds an annotation which lists samples with a novel allele (INFO/NOVELAL) or a novel genotype (INFO/NOVELGT)

counts

A minimal plugin which counts number of samples, SNPs, INDELs, MNPs and total number of sites.

dosage

Prints genotype dosage determined from FORMAT/PL, GL, or GT.

fill-from-fasta

Fills INFO or REF field based on values in a fasta file.

fill-tags

Sets INFO tags such as AF, AC, AC_Hemi, etc, for all samples or per population.

fixploidy

Fix ploidy

fixref

Diagnose and fix VCFs with genotypes on incorrect strand.

frameshifts

Annotates frameshift indels.

GTisec

Counts genotype intersections across all possible sample subsets in a vcf file.

GTsubset

Outputs sites where the requested samples all exclusively share a genotype (GT), i.e. all selected samples must have the same GT, while non of the others can have it.

guess-ploidy

Determines sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT) in the non-PAR region of chrX.

impute-info

Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available.

isecGT

Compares two files and set non-identical genotypes in the first file to missing.

mendelian

Count Mendelian consistent / inconsistent genotypes

prune

Prunes sites by missingness or linkage disequilibrium.

setGT

Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that.

tag2tag

Converts between similar tags, such as GL, PL and GP.

trio-switch-rate

Calculates phase switch rate in trio children.

Feedback

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