MakeMixtureVcf

Overview

Group: VCF/BCF

Creates a VCF with one sample whose genotypes are a mixture of other samples’.

The input VCF must contain all samples to be mixed, and may optionally contain other samples. Sample mixtures can be specified in one of several ways:

1. --samples s1 s2 s3: specifies that the samples with names s1, s2 and s3 should be mixed equally.
2. ` –samples s1@0.1 s2@0.1 s3@0.8: specifies that the three samples should be mixed at 0.1, 0.1, and 0.8` respectively
3. --samples s1@0.1 s2 s3: specifies that s1 should form 0.1 of the mixture and that the remaining (0.9) should be equally split amongst s2 and s3
4. If no sample names are given, all samples in the input VCF will be used, mixing equally

The input samples are assumed to be diploid with the allele fraction defined by the genotype (0/0, 0/1 or 1/1). The --allele-fraction-field option may be specified, in which case the allele fraction of the input genotypes will be retrieved from the specified FORMAT field in the VCF genotypes. All genotypes except hom-ref and no-call genotypes must have this field present if supplied.

If the –no-call-is-hom-ref flag is true (the default) then no-call genotypes in the input VCF are interpreted as hom-ref genotypes. If it is false, any location with a no-call genotype will be emitted as a no-call in the mixture, and will be filtered.

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToVcf	Input VCF containing genotypes for the samples to be mixed.	Required	1
output	o	PathToVcf	Output VCF of mixture sample.	Required	1
samples	s	String	Samples to mix. See general usage for format and examples.	Optional	Unlimited
output-sample-name	S	String	Output sample name.	Optional	1	mixture
no-call-is-hom-ref	N	Boolean	Treat no-calls for samples as hom-ref genotypes.	Optional	1	true
allele-fraction-field	a	String	Format field containing allele fraction.	Optional	1
precision	p	Int	Digits of precision in generated allele fractions.	Optional	1	5