MakeTwoSampleMixtureVcf

Overview

Group: VCF/BCF

Creates a simulated tumor or tumor/normal VCF by in-silico mixing genotypes from two samples.

The tumor genotypes are created by mixing the incoming genotypes for the for the ‘tumor’ sample and the incoming genotypes for the ‘normal’ samples with the ‘tumor’ alleles accounting for tumorFraction of the resulting mixture and the ‘normal’ alleles accounting for 1 - tumorFraction of the resulting mixture (see --tumor-fraction). E.g. if the ‘tumor’ genotype is A/C, the ‘normal’ genotype is C/C, and ‘tumorFraction’ is set at 0.5, then the resulting tumor genotype will be A/C with an allele fraction of 0.75. The resulting allele fraction is written to the AF info field in the VCF.

In tumor-only mode (--tumor-only) only tumor genotypes are output. In tumor/normal mode genotypes for the ‘normal’ samples are also emitted, and match the genotypes from the input sample.

All loci (potentially restricted by intervals) that are variant in one or both samples are written to the output VCF, though in several cases the variants will be filtered:

• If either of the tumor or normal sample is no-called the resulting locus will have the unknown_gt filter applied
• If the tumor and the normal have more than one alternative allele between them the multi_allelic filter will be applied
• In tumor/normal mode (as opposed to tumor-only) loci that have an alt allele in the normal sample will have the alt_allele_in_normal filter applied

Arguments

Name	Flag	Type	Description	Required?	Max # of Values	Default Value(s)
input	i	PathToVcf	Input VCF file.	Required	1
output	o	PathToVcf	Output VCF file.	Required	1
tumor	t	String	Name of the ‘tumor’ sample in the input VCF.	Required	1
normal	n	String	Name of the ‘normal’ sample in the input VCF.	Required	1
tumor-fraction	f	Double	What fraction of the mixture comes from the ‘tumor’ sample.	Optional	1	0.5
tumor-only	T	Boolean	Tumor only mode - only output tumor genotypes and don’t filter sites.	Optional	1	false
no-call-is-hom-ref	N	Boolean	Treat no-calls for either sample as hom-ref genotypes.	Optional	1	true
intervals	l	PathToIntervals	Optional set of intervals to restrict to.	Optional	1