Error getting the genome on clinvaR

Question

[camillab.]

Hi,

I am trying to use clinvaR following this vignette (here ) but when I try to download and Import 1000 Genomes VCF, I get an error:

Cannot open specified tabix file: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
Error in read.table(text = paste(output, collapse = "\n"), header = F,  : 
  no lines available in input

What I am doing wrong?

Thank you Camilla

[Ram]

Your vignette URL is on your localhost, no one but you can access that URL.

[camillab.]

sorry! I got the link typing on R browseVignettes(package = "clinvaR")

Answer 1

[Pierre Lindenbaum]

I don't think tabix supports the FTP protocol. Try http :

https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

[camillab.]

thank you for the help! Where I am suppose to add the http? I tried to use the assembled a compilation of gene list as suggested by the tutorial (from browseVignettes(package = "clinvaR") ) :

 hcm_panel2 <- get_genes('lmm_hcm.tsv')
    print(hcm_panel2) #ok it gives me the genes that I want
    vcf <- import_file_1000g(genes = hcm_panel2)

it says Error in system(sprintf("ls %s/1000G", dir), intern = T) : 'ls' not found

and even if I try to get_date_list() I get an error saying:

Error in system(sprintf("ls %s/Archive_Tables", dir), intern = T) : 
  'ls' not found

[Ram]

Are you on Windows?

[camillab.]

yes I am! is it a problem?

[Ram]

Looks like it - the package is trying to run ls which is not a command on Windows. Is this you on their GitHub? https://github.com/jamesdiao/clinvaR/issues/1

[camillab.]

yes it was me (I tried to the developers before bother people here). so if I want it to run it, I will have to use it on Mac?

[Ram]

Yes, or overwrite that function with another that is adapted for Windows.

[camillab.]

I wish I know how to do that! but thank you! I will use a mac to run it! hopefully it will work! Mistery solved!