Created
June 19, 2021 17:46
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Read genotype data for given range from VCF and convert to dosage matrix
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require(VariantAnnotation) | |
require(GenomicRanges) | |
get_cis_geno = function(tab, chrom, left, right, genome_build = "GRCh38") { | |
gr = GRanges(chrom, IRanges(left, right)) | |
sp = ScanVcfParam(which = gr) | |
vcf = readVcf(tab, genome_build, param = sp) | |
gt = geno(vcf)$GT | |
if (nrow(gt) == 0) return(NULL) | |
allele1 = substr(gt, 1, 1) | |
class(allele1) = "numeric" | |
allele2 = substr(gt, 3, 3) | |
class(allele2) = "numeric" | |
allele1 + allele2 | |
} | |
tab = TabixFile("the.vcf.gz", "the.vcf.gz.tbi") | |
dosage_matrix = get_cis_geno(tab, “chr1”, 100000, 101000) |
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