R, PopGenome Package. Cannot open file

Question

[pifferdavide]

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

[pifferdavide]

I have both files in the same folder and I downloaded from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

[huan1920]

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?

[bastianxpfeifer]

Hi ALL, see also http://popgenome.weebly.com/

THX, all the best.

Bastian

Answer 1

[Ram]

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

[pifferdavide]

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

[Ram]

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

[pifferdavide]

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

[Ram]

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)

[pifferdavide]

I tired it but I get no output