Question

VariantAnnotation: Error with ScanVcfParam

0

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Didi ▴ 10

@didi-10905

Last seen 2.8 years 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 • 2.9k views

ADD COMMENT • link 7.4 years ago Didi ▴ 10

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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.

ADD REPLY • link 7.4 years ago Didi ▴ 10

0

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

ADD REPLY • link 7.4 years ago Michael Lawrence ★ 11k

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It's working.

Thanks a lot.

ADD REPLY • link 7.4 years ago Didi ▴ 10

score 1 · Answer 1 · 2017-08-04

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Valerie Obenchain ★ 6.8k

@valerie-obenchain-4275

Last seen 2.9 years 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

ADD COMMENT • link 7.4 years ago Valerie Obenchain ★ 6.8k

1

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And it's easy to check using

headerTabix(filename)$seqnames

ADD REPLY • link 7.4 years ago Michael Lawrence ★ 11k

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.

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.

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.