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FMT/DP of missing genotypes

snp bcftools filtering variantannotation depth written 29 days ago by scottbrainard • 30

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114

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incompatibility of variant positions between my data and databases

annovar next-gen sequence variantannotation snp written 3 months ago by siinemselvi • 0

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308

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Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotation?

exome vcf snpeff vep variantannotation written 8 months ago by svp • 420

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294

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Read genotype information with VariantAnnotation

vcf R bioconductor snp variantannotation written 9 months ago by jeni • 40 • updated 9 months ago by benformatics • 2.1k

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892

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Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)

vcf bioconductor variantannotation written 2.1 years ago by ricardoguerreiro2121 • 60

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601

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locateVariants returns an empty result

indel R bioconductor variantannotation written 2.9 years ago by boris • 0

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1.9k

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ReadVCF not reading samples

R readvcf variantannotation written 5.8 years ago by Alexander Skates • 360 • updated 3.2 years ago by Biostar ♦♦ 20

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1.3k

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Unable to read large Vcf file in R

R variantannotation vcf files written 3.7 years ago by sridevi • 0

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2.4k

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How to make new VCF files myself?

vcf variant variantannotation written 4.5 years ago by Amirosein • 70 • updated 4.4 years ago by chen • 2.1k

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2.0k

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VariantAnnotation: error from readVcf command

R variantannotation written 5.8 years ago by pifferdavide • 100

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5.5k

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How can I filter a vcf file by DP and GQ using the R package VariantAnnotation?

vcf R bioconductor variantannotation written 6.0 years ago by r.jaffe • 10 • updated 6.0 years ago by Jeremy Leipzig ♦ 19k

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Recent Replies

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There is a [new pre-print from Hippen et al.][1] that proposes an adaptive probabilistic approach...
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If there are more than 5 factor levels for age, you could perhaps try adding age as a random effect.
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What is the relationship between current fasta header and expected one?
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Hi Shenwei seqkit replace -k acc2gi.tsv -p "^(.+?) (.+)$" -r "gi|{kv}|ref|\$1| \$2" seqs.fas...
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hhh, I have decided to use vscode-R :)
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1) biologically speaking that would mean (eukaryotic case) that you would have a single 'sequence...
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At what point in the analysis are you starting from, and what files do you currently have?
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Hi, I have tried the package, it was pretty great although there are some mistakes in the Rcode (...
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I think that you mean the values from computeMatrix function. You should have as many lines as t...
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> "A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No ov...
C: Getting mitochondrial genes for scRNAseq by ATpoint ♦ 46k
That would still qualify the cell (=the droplet) as poor quality, so where is the difference in u...
C: Plink1.07 generate ERRORs when reading covaries by heqianchange • 0
Thank you very much. I revised the format of the covariable file and the error has gone.

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