PopGenome...ReadVCF. Cannot open the file. Why?
I downloaded 1000 Genomes data. I put both the .tbi and the .vcf file in the same folder. However, I get this error message when I try to read the file.
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'):
'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
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pifferdavide
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Should it be chr22.vcf perhaps? R cant find a file the the name you passed.
I typed:
Still get the same error message!
I'm pretty sure he meant
readVCF("C:/Users/Davide/Documents/Chr22/chr22.vcf", 1000,"22",1,100000)In any case, ensure that the capitalization is correct.
This is the PopGenome package guide: http://www.inside-r.org/packages/cran/PopGenome/docs/readVCF
Try indexing it first. It's looking for the index for that file.
Ok I am a NOOB. How do I index it?
I downloaded chr21 to see if there was something wrong with the file. File extensions seem OK. Attached screenshot of files!