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Question: VariantAnnotation: Error with ScanVcfParam
0
gravatar for Didi
3 months ago by
Didi10
Didi10 wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Didi10
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.

ADD REPLYlink modified 3 months ago • written 3 months ago by Didi10

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

ADD REPLYlink written 3 months ago by Michael Lawrence9.8k

It's working. 

Thanks a lot.

 

ADD REPLYlink written 3 months ago by Didi10
1
gravatar for Valerie Obenchain
3 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

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

ADD COMMENTlink written 3 months ago by Valerie Obenchain ♦♦ 6.4k
1

And it's easy to check using 

headerTabix(filename)$seqnames

 

ADD REPLYlink written 3 months ago by Michael Lawrence9.8k
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