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R, PopGenome Package. Cannot open file

I downloaded the Chromosome in vcf format along with the tbi file from 1000 Genomes ftp server. I installed the packaged "PopGenome". However, I cannot open the files. I type this command and get an error message. Am I missing something?

readVCF("C:/Users/Davide/Documents/chr22/Chr22.vcf", 1000,"22",1,100000)
open: No such file or directory
Caught exception inside whop_tabix::open('C:/Users/Davide/Documents/chr22/Chr22.vcf.gz"):
    'whop_tabix::open : Failed to open tabix index file'
return FALSE from whoptabix_open
vcff::open : could not open tabix-index!
VCF_open : Could not open file 'C:/Users/Davide/Documents/chr22/Chr22.vcf' as tabix-indexed!
[1] FALSE
snp popgenome r
• 6,126 views • link
updated by Ram Ram • written by pifferdavide pifferdavide

Did you try this: GENOME.class=readVCF() instead of just readVCF()?

By the way, the example.VCF file didn't have a tabix-index file with it, why it can load in successfully?

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updated by Ram Ram • written by huan1920 • huan1920

1 answer

You should have a Chr22.vcf.tbi tabix index in the same folder as the VCF file. If that doesn't exist, you can always create one as shown here: http://samtools.sourceforge.net/tabix.shtml

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written by Ram Ram

I do have a Chr22.vcf.tbi tabix index in the same folder.

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written by pifferdavide pifferdavide

Can you check the permissions on the file please? Also Windows might set security flags on downloaded files that you might have to "unblock".

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written by Ram Ram

You were indeed right but it's still not working, even after I unblocked both files...still getting same error message!

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written by pifferdavide pifferdavide

Can you try, on R:

Sys.chmod("C:/Users/Davide/Documents/chr22/Chr22.vcf", mode = "0777",showWarnings=TRUE)
Sys.chmod("C:/Users/Davide/Documents/chr22/Chr22.vcf.tbi", mode = "0777",showWarnings=TRUE)
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written by Ram Ram

I tired it but I get no output

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written by pifferdavide pifferdavide

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