User: Anna N.

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Anna N. 0
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Posts by Anna N.

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Answer: A: VariantAnnotation package, subseting vcfs on fixed fields
... much obliged! I can filter my vcfs using other tools, but I would prefer to have a full pipeline using VariantAnnotation.   Anna ...
written 4.8 years ago by Anna N. 0
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VariantAnnotation package, subseting vcfs on fixed fields
... Hello I have a large vcf file and I would like to keep only the pass entries in the filter column. Is there a way to do this with Variant Annotation? I know that we can subset on the fields eg ## Subset on 'fixed', 'info' or 'geno' fields: param <- ScanVcfParam(fixed="ALT", geno=c("GT", "H ...
variantannotation vcf fixed filter written 4.8 years ago by Anna N. 0
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Answer: A: VariantAnnotation _ problem in merging files, mutationspectrum per sample
...                  I used a different set of samples and I encountered the same problems- when I use the tsv output, after readMutect and merging, my matrix from the motifMatrix function looks like that:                 sample1       sample2      sample3     sample4      sample5     sample6       sa ...
written 4.9 years ago by Anna N. 0
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Comment: C: VariantAnnotation _ problem in merging files, mutationspectrum per sample
... Hi Julian I edited the post, hope it is fine now. I will try to explain a little better my problem. The tsv files are Mutect's output, so I can use the readMutect command. When I merge, the sample names are retained and I can plot the spectrum per sample _ meaning that I end up with a spectrum t ...
written 4.9 years ago by Anna N. 0
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VariantAnnotation _ problem in merging files, mutationspectrum per sample
... Hello again I have encountered some problems and I would like your valuable input. My analysis pipeline produces either tsv file per patient/sample or vcf file. Since I wanted to have all my patients in one file I tried several approaches. I have samples that are different and also they don't ha ...
variantannotation written 4.9 years ago by Anna N. 0 • updated 4.9 years ago by Julian Gehring1.3k
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Answer: A: Import of vcf with VariantAnnotation
... Thank you for all the help! I am waiting to update my packages and start over Anna   ...
written 5.0 years ago by Anna N. 0
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Answer: A: Import of vcf with VariantAnnotation
... Hello Valerie,   The file is in my working directory, even if I include the full pathway I have the same problems... I am sending you the file in your email Thank you very much Anna ...
written 5.0 years ago by Anna N. 0
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Answer: A: Import of vcf with VariantAnnotation
...  Hi Valerie, no I am not able to read the file with scanVcf(fl) and it is not a big file (325 kb) I am pasting the sessionInfo() > fl=readVcf("Ac216_H69_1_A549_mutect_confident_eff.vcf", "hg19") Error in FUN(X[[2L]], ...) : subscript out of bounds In addition: Warning message: In ...
written 5.0 years ago by Anna N. 0
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Import of vcf with VariantAnnotation
... Hello again,   after installing succesfully the packages and reproducing all examples, I would like to analyze my own mutation calls. I have a problem importing my vcf file - sorry if these are naive questions but I am really new here.   > fl=readVcf("Ac216_H69_1_A549_mutect_confident_eff.v ...
variantannotation somaticsignatures written 5.0 years ago by Anna N. 0
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Answer: A: SomaticSignatures, cannot reproduce use case
... Dear Wolfgang thank you for your answer. Apparently I was missing a dependency: the package checkmate - so this is why VariantAnnotation was not loading properly. Now everything is working like a charm. Thank you all for your answers and help. Anna ...
written 5.0 years ago by Anna N. 0

Latest awards to Anna N.

Popular Question 4.7 years ago, created a question with more than 1,000 views. For Import of vcf with VariantAnnotation
Popular Question 4.7 years ago, created a question with more than 1,000 views. For SomaticSignatures, cannot reproduce use case
Popular Question 4.7 years ago, created a question with more than 1,000 views. For SomaticSignatures, cannot reproduce use case
Scholar 4.9 years ago, created an answer that has been accepted. For A: Import of vcf with VariantAnnotation

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