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parallel genCountMatrixFromVcf
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| 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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