customProDB: issues getting dbSNP data for human (hg19)
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@kristenbeck527-8349
Last seen 6.2 years ago
United States

I am trying to use the variant annotation capabilities in customProDB. I would like to make a variant annotated fasta file, but I am running into issues retrieving the dbsnp data for hg19.

PrepareAnnotationRefseq(genome='hg19', CDSfasta, pepfasta, 
     annotation_path=annotation_path_hs, splice_matrix = FALSE, 
     dbsnp = "snp130", COSMIC = TRUE)

I also tried "snp131" as recommended in the vignette and "snp135" as recommended in the help page of the function. All snp variations returned the error below.

Error in PrepareAnnotationRefseq(genome = "hg19", CDSfasta, pepfasta,  : 
  invalid dbsnp name for specified genome

Any help would be appreciated. Thank you!

 

 

customprodb dbsnp refseq varianttools • 952 views
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@xiaojingwang-8081
Last seen 3.1 years ago
United States
Try using ‘snp138’, ‘snp141’ or ‘snp142’ instead. You may use the code below to check the current dbSNP version provided by the UCSC table browser. I’ll update the document accordingly. library(rtracklayer) session <- browserSession() genome(session) <- 'hg19' tmp <- trackNames(session) tmp[grep('snp', tmp)] xiaojing From: kristenbeck527 [bioc] [mailto:noreply@bioconductor.org] Sent: Wednesday, July 08, 2015 5:10 PM To: Wang, Xiaojing Subject: [bioc] customProDB: issues getting dbSNP data for human (hg19) Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User kristenbeck527<https: support.bioconductor.org="" u="" 8349=""/> wrote Question: customProDB: issues getting dbSNP data for human (hg19)<https: support.bioconductor.org="" p="" 69670=""/>: I am trying to use the variant annotation capabilities in customProDB. I would like to make a variant annotated fasta file, but I am running into issues retrieving the dbsnp data for hg19. PrepareAnnotationRefseq(genome='hg19', CDSfasta, pepfasta, annotation_path=annotation_path_hs, splice_matrix = FALSE, dbsnp = "snp130", COSMIC = TRUE) I also tried "snp131" as recommended in the vignette and "snp135" as recommended in the help page of the function. All snp variations returned the error below. Error in PrepareAnnotationRefseq(genome = "hg19", CDSfasta, pepfasta, : invalid dbsnp name for specified genome Any help would be appreciated. Thank you! ________________________________ Post tags: customprodb, dbsnp, refseq, varianttools You may reply via email or visit customProDB: issues getting dbSNP data for human (hg19)
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Thank you for your response! It worked with "snp138" and your code provided helped me to better understand the genome in this session.

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