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

add VariantKey INFO fields VKX and RSX

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

count the frequency of the length of REF, ALT and REF+ALT

Checks if ploidy of samples is consistent for all sites.

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

Colors shared chromosomal segments shared. Requires phased GTs.

Runs a basic association test, per-site or in a region, and checks for novel alleles and genotypes in two groups of samples. Adds the following INFO annotations:

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

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

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

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

Fix ploidy

Diagnose and fix VCFs with genotypes on incorrect strand.

Annotates frameshift indels.

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

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.

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

compress gVCF file by resizing non-variant blocks according to specified criteria

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.

Calculates per-sample or de novo indels stats. The usage and format is similar to smpl-stats and trio-stats.

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

Count Mendelian consistent / inconsistent genotypes

sets missing genotypes ("./.") to ref allele ("0/0" or "0|0"). DEPRECATED, use setGT instead.

determine parental origin of a CNV region

Prune sites by missingness, allele frequency or linkage disequilibrium. Alternatively, annotate sites with r2, Lewontin’s D' (PMID:19433632), Ragsdale’s D (PMID:31697386).

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

calculates basic per-sample stats. The usage and format is similar to indel-stats and trio-stats.

split VCF by sample, creating single-sample VCFs

extract fields from structured annotations such as INFO/CSQ created by bcftools/csq or VEP. These can be added as a new INFO field to the VCF or in a custom text format

Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD.

screen variants for possible de-novo mutations in trios

Calculate transmission rate in trio children. The usage and format is similar to indel-stats and smpl-stats.

Calculates phase switch rate in trio children.

generate unsorted VariantKey-RSid index files in hexadecimal format