User: sebastian.hollizeck

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Posts by sebastian.hollizeck

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Comment: C: VariantAnnotation - expand not working as intended for VCF
... This is the solution, ty so much! I just found no documentation what so ever to access expanded vcfs and expected them to work according to the normal vcfs. Especially since if I just use geno(evcf)$AD it returns just a one dimensional vector, which is kinda counter intuitive ...
written 9 months ago by sebastian.hollizeck0
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Comment: C: VariantAnnotation - expand not working as intended for VCF
... Here the header plus one of the lines, that show this behaviour http://pastebin.com/f0hVctUG ...
written 9 months ago by sebastian.hollizeck0
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Comment: C: VariantAnnotation - expand not working as intended for VCF
... > vcf class: CollapsedVCF dim: 61872 1 rowRanges(vcf): GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER info(vcf): DataFrame with 23 columns: AC, AF, AN, BaseQRankSum, ClippingRankSum, DP, ... info(header(vcf)): Number Type Description ...
written 9 months ago by sebastian.hollizeck0
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VariantAnnotation - expand not working as intended for VCF
... Hi, as I am currently working on creating a new database for the variants called in our cohort, I stumbled upon the expand function in VariantAnnotation for the vcf object expand(x, ..., row.names = FALSE): Expand (unlist) the ALT column of a CollapsedVCF object to one row per ALT value. Variables ...
variantannotation written 9 months ago by sebastian.hollizeck0 • updated 9 months ago by Michael Lawrence9.8k

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