User: ruben.drews

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Posts by ruben.drews

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Answer: A: Best way to create a VRanges object from a large VCF file?
... Decided to do it the quick-and-dirty way. For the sake of this community, I'll post my solution but it's not pretty. For my 5,000,000x80 it takes around 20-25 minutes.    inputLargeVcfFile=function(vcfFile){ # Get samples from VCF file hvcf=scanVcfHeader(vcfFile) sampleNames=samples( ...
written 6 weeks ago by ruben.drews0
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Comment: A: Best way to create a VRanges object from a large VCF file?
... Thanks for the quick answer!   Method#2: Yes, I basically filter for "." in the GT field: vcfTemp=readVcfAsVRanges(vcfFile, genome="mm10", param) vcfTempFiltered=vcfTemp[which(vcfTemp$GT!=".")] But then I cannot append or merge the files from the list of VRanges objects together.   Current ...
written 6 weeks ago by ruben.drews0
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Best way to create a VRanges object from a large VCF file?
... Hi all, I got from my collaborators a VCF file which contains all SNVs from all samples. The rows depict the SNVs and the columns depict the mutational status in all samples. Naturally, it is a sparse matrix. Here is an example line:   #CHROM POS ID REF ALT QUAL FILTER INFO ...
vcf variantannotation readvcfasvranges readvcf written 6 weeks ago by ruben.drews0 • updated 6 weeks ago by Michael Lawrence8.9k

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