User: sskimb

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sskimb10
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Posts by sskimb

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readVcf: duplicated records produced importing 1kG vcf
... I would like to report a bug in readVcf (VariantAnnotation). This bug produces duplicated records when reading [1000 Genomes Phase3 vcf files][1]. Here is a minimal code that reproduces the bug: ``` > library(VariantAnnotation) > ikGFile <- "/data/1kG/ALL.chr21.phase3_shapeit2_mvncall_inte ...
software error written 4 months ago by sskimb10
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Genome versions of the VcfFiles from AnnotationHub
... 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 ...
annotation annotationhub software error vcf written 3.6 years ago by sskimb10 • updated 3.6 years ago by Valerie Obenchain6.7k

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