getSexFromVcf: Get sample sex from a VCF file

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Get sample sex from a VCF file

Description

This function detects non-random distribution of homozygous variants on chromosome X compared to all other chromosomes. A non-significant Fisher's exact p-value indicates more than one chromosome X copy. This function is called in runAbsoluteCN as sanity check when a VCF is provided. It is also useful for determining sex when no sex marker genes on chrY (e.g. AMELY) are available.

Usage

getSexFromVcf(
  vcf,
  tumor.id.in.vcf = NULL,
  min.or = 4,
  min.or.na = 2.5,
  max.pv = 0.001,
  homozygous.cutoff = 0.95,
  af.cutoff = 0.2,
  min.coverage = 15,
  use.somatic.status = TRUE
)

Arguments

vcf	CollapsedVCF object, read in with the readVcf function from the VariantAnnotation package.
tumor.id.in.vcf	The tumor id in the CollapsedVCF (optional).
min.or	Minimum odds-ratio to call sample as male. If p-value is not significant due to a small number of SNPs on chromosome X, sample will be called as NA even when odds-ratio exceeds this cutoff.
min.or.na	Minimum odds-ratio to not call a sample. Odds-ratios in the range min.or.na to min.or define a grey area in which samples are not called. Contamination can be a source of ambiguous calls.
max.pv	Maximum Fisher's exact p-value to call sample as male.
homozygous.cutoff	Minimum allelic fraction to call position homozygous.
af.cutoff	Remove all SNVs with allelic fraction lower than the specified value.
min.coverage	Minimum coverage in tumor. Variants with lower coverage are ignored.
use.somatic.status	If somatic status and germline data is available, then exclude somatic variants.

Value

Returns a character(1) with M for male, F for female, or NA if unknown.

Author(s)

Markus Riester

See Also

getSexFromCoverage

Examples

vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
vcf <- readVcf(vcf.file, "hg19")
# This example vcf is filtered and contains no homozygous calls,
# which are necessary for determining sex from chromosome X.
getSexFromVcf(vcf)

lima1/PureCN documentation built on April 24, 2024, 8:23 p.m.