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Posts by sskimb
... I would like to report a bug in readVcf (VariantAnnotation). This bug produces duplicated records when reading [1000 Genomes Phase3 vcf files]. Here is a minimal code that reproduces the bug: ``` > library(VariantAnnotation) > ikGFile <- "/data/1kG/ALL.chr21.phase3_shapeit2_mvncall_inte ...
... I found that the genome build of the VcfFiles downloaded from AnnotationHub is obscure: the genome and tags fields mismatch as shown below. > library(AnnotationHub) > ah <- AnnotationHub() > vfs <- query(ah, 'VcfFile') > mcols(vfs)[, c(1,5,7)] DataFrame with 8 rows and 3 colu ...
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