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rvalieris/parallel_count_matrix.R

Last active June 20, 2018 18:17
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parallel genCountMatrixFromVcf
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parallel_count_matrix.R
library(signeR)
library(VariantAnnotation)
library(BSgenome.Hsapiens.UCSC.hg19)
library(BiocParallel)
register(MulticoreParam(workers=5)) # use 5 cores
vcf = readVcf("a.vcf")
split_vcf = split(vcf,ceiling(seq_along(vcf)/1000)) # split vcf into chunks of 1000 rows
split_r = bplapply(split_vcf, function(p){genCountMatrixFromVcf(BSgenome.Hsapiens.UCSC.hg19, p)})
result_matrix = Reduce('+', split_r)
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