User: r.jaffe

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r.jaffe0
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Posts by r.jaffe

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Comment: C: Question: How can I filter a vcf file by DP and GQ using the R package VariantAn
... Hi Martin, thanks for your reply. If I do what you suggest I get this error: Error in NSBS(i = i, x = x, exact = exact, upperBoundIsStrict = upperBoundIsStrict) : subscript is a logical vector with out-of-bounds TRUE values In addition: Warning message: In NSBS(i, x, exact = exact, upperBoundIs ...
written 3.2 years ago by r.jaffe0
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Question: How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?
... Hi guys, need some help filtering my vcf files with the VariantAnnotation package (v1.12.9) from Bioconductor. I have a vcf file (v4.2) containing 28238 SNPs for 160 individuals, and I'm running R version 3.1.3 I opened my file and ran: hist(geno(vcf)$DP) ##check the distribution of Read Depth his ...
variantannotation vcf sample read depth phred-scaled genotype quality written 3.2 years ago by r.jaffe0 • updated 3.2 years ago by Valerie Obenchain ♦♦ 6.5k

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