ref.al.freq: Compute reference STR allele frequencies from a vcf file.

In jk2236/RecordMatching: Statistical detection of relatives typed with disjoint forensic and biomedical loci

Description

This function extract STR allele frequences from reference vcf file (ref.f) with vcftools.

Usage

ref.al.freq(ref.f, marker)

Arguments

ref.f	A name (including full path) of a file containing SNP-STR haplotypes to be used as a reference panel for imputation. Note that the reference panel must be phased and have no missing values.
marker	STR marker name of which allele frequency is computed.

Details

The STR allele frequency is necessary for computing match scores. The output file is saved under ref_alfrq folder within the base folder. The output file name is ref_(marker).frq format.

Value

None

See Also

vcftools manual.

jk2236/RecordMatching documentation built on Dec. 21, 2021, 12:10 a.m.