look1kg: query 1000 genomes genotypes at pairs of SNP

In vjcitn/BiocRnaHap: explore RNA-seq based haplotyping using Phaser

Description

query 1000 genomes genotypes at pairs of SNP

Usage

look1kg(rsids = c("rs71503074", "rs71503075", "rs12084944"),
  ch = BiocRnaHap::ch38to19,
  src = "http://1000genomes.s3.amazonaws.com/release/20130502/ALL.%s.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz",
  rsonly = TRUE, snvonly = TRUE)

Arguments

rsids	character vector
ch	chain object from rtracklayer
src	character(1) sprintf template for 1000 genomes vcf, chr[nn] to be supplied for pct-s
rsonly	logical(1), exclude 'esv' records
snvonly	logical(1), exclude records with nchar(REF)>1

Note

Typically SNPs are identified by rs number, but there are some workstreams in which they come back as snp_cc_lllll where cc is a chromosome identifier and lllll is a location. We parse the 'rsids' input for '^snp' and if we find this we skip the step of resolving the rsid to genomic coordinates, using the cc and lllll for location.

Examples

lk2 = look1kg(c("rs71503074","rs71503075","rs12084944"))
table(geno(lk2)$GT[1,], geno(lk2)$GT[2,], geno(lk2)$GT[3,])

vjcitn/BiocRnaHap documentation built on June 17, 2019, 9:31 p.m.