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CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf customprodb gatk snv inputvcf written 10 weeks ago by Elena.M • 0
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rbind VCF Two Objects Column Names Error
variantannotation vcf written 3 months ago by Dario Strbenac • 1.5k
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109
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Help creating VRange object
somaticsignatures vcf vrange written 4 months ago by maisapinheiro12 • 0 • updated 4 months ago by Julian Gehring • 1.3k
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VCF file does not include snp.id, can I still run SNPRelate for Relatedness Analysis? Data is output from STACKS for mangroves
snprelate vcf written 5 months ago by cav3gh • 0 • updated 5 months ago by Stephanie M. Gogarten • 680
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Bioconductor and WGS: recommended practices?
vcf variants wgs whole genome sequencing written 7 months ago by Vincent J. Carey, Jr. ♦ 6.3k
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vcf to venn diagram
vcf snps venn diagram ggplot2 written 8 months ago by mictadlo • 0
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Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges written 14 months ago by david.mas • 0 • updated 14 months ago by Michael Lawrence ♦ 11k
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comparing 2 long BED files in R in an efficient way
vcf bed written 14 months ago by Bogdan • 580 • updated 14 months ago by GENOMIC_region • 0
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400
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Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
vcf snps motifbreakr motif analysis written 15 months ago by svlachavas • 700 • updated 15 months ago by Valerie Obenchain • 6.7k
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PureCN use of VCF QUAL column for filtering when column is dot
vcf purecn qual written 16 months ago by twtoal • 0 • updated 16 months ago by markus.riester • 110
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338
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VCF file non-SNP germline mutations
snp vcf purecn written 17 months ago by twtoal • 0 • updated 17 months ago by markus.riester • 110
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Error converting vcf to gds
snprelate vcf gds written 18 months ago by annat22 • 0 • updated 17 months ago by zhengx • 30
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VariantAnnotation: Error with ScanVcfParam
variantannotation vcf readvcf filtervcf scanvcfparam written 2.1 years ago by Didi • 10
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extracting Allele Read Counts
rsamtools vcf written 2.5 years ago by Bogdan • 580
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Select specific variants from vcf file
vcf written 2.5 years ago by Adam • 0 • updated 2.5 years ago by Martin Morgan ♦♦ 23k
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472
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Error in matrix
vcf bioconductor written 2.5 years ago by bkauf • 0
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merge vcf files with different samples and variants?
vcf written 2.5 years ago by shilin.zhao • 30
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Any tool to calculate Fst on haploid data?
vcf snps written 2.6 years ago by rkdonthu • 10
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Best way to create a VRanges object from a large VCF file?
variantannotation vcf readvcf readvcfasvranges written 2.7 years ago by ruben.drews • 0 • updated 2.7 years ago by Michael Lawrence ♦ 11k
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about the use of subsetByFilter()
vcf written 2.7 years ago by Bogdan • 580 • updated 2.7 years ago by Martin Morgan ♦♦ 23k
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about collapsed and expanded vcf file
vcf written 2.7 years ago by Bogdan • 580 • updated 2.7 years ago by raggieapauly • 0
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3
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596
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about filtering variants from a VCF file
vcf written 2.7 years ago by Bogdan • 580
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452
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CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
variantannotation vcf written 2.8 years ago by Sean Davis ♦ 21k • updated 2.7 years ago by Valerie Obenchain • 6.7k
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567
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vcfR package vector length error
vcf written 2.9 years ago by jenniewoo • 20 • updated 2.9 years ago by Martin Morgan ♦♦ 23k
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587
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annotating a vcf file containing Structural Variants
vcf written 3.0 years ago by Bogdan • 580
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