VariantAnnotation: Error with ScanVcfParam
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Didi ▴ 10
@didi-10905
Last seen 12 weeks ago
Spain

Hi,

I tried to get from the VCF file the SNPs that are in chr5 between 3-6Mb using this script and I've got this error.

library(VariantAnnotation)
library(Rsamtools)
VARvcf <- readVcf("/media/Data/VAR_reads (Variants).vcf.gz")
idx <- indexTabix("/media/Data/VAR_reads (Variants).vcf.gz", "vcf")

tab <- TabixFile("/media/Data/VAR_reads (Variants).vcf.gz", idx)

param <- ScanVcfParam(which = GRanges("chr5", IRanges(3000000, 6000000)))
VARvcf_rng <- readVcf(tab, param=param)

Error: scanVcf: scanVcf: scanTabix: 'chr5' not present in tabix index
path: /media/Data/VAR_reads (Variants).vcf.gz

index: /media/Data/VAR_reads (Variants).vcf.gz.tbi

  path: /media/Data/VAR_reads (Variants).vcf.gz

Is there something wrong with the script?

Thanks a lot.

D.

variantannotation vcf readvcf filtervcf scanvcfparam • 1.8k views
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Hi, 
I checked and everything seems ok.

headerTabix(tab)$seqnames
 [1] "Chr1"  "Chr2"  "Chr3"  "Chr4"  "Chr5"  "Chr6"  "Chr7"  "Chr8"  "Chr9"  "Chr10"
[11] "Chr11" "Chr12"

I still don't know what's the problem.

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Note the capitalization. You'll need to use "Chr5" when constructing your GRanges.

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It's working. 

Thanks a lot.

 

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@valerie-obenchain-4275
Last seen 4 months ago
United States

The error says the tabix file doesn't have a chromosome named 'chr5'. Is this true? Have you checked the file to see how the chromosome names are represented? Depending on how the file was generated it might have just '5' with no 'chr' prefix or maybe there isn't any chromosome 5 data in there.

Valerie

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And it's easy to check using 

headerTabix(filename)$seqnames

 

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