I am working on importing this SNP data into IGV and have been running into problems left and right. I have downloaded the file from the FTP site. I have tried multiple methods, to no avail.
When I unzip the file and attempt to import it into IGV I get an error message: "Unknown file type: C:...\snpBatch_ENSEMBL_1050082 Check file extension"
When I rename that unzipped file to a .gff and attempt import , I am prompted to create an index for the file. When I accept, I receive an error message: "Failed to parse line -1: ss# loc_snp_id allele samplesize rs# ss2rs_orien chr chr_pos contig_acc contig_pos rs2genome_orien assembly weight Column 4 must contain a numeric value. For input string: " samplesize"
If I use IGVtools to create a .tdf file, I receive: "Error loading C:...\snpBatch_ENSEMBL_1050082.tdf: null"
Finally, if I try to import directly from the dbSNP's FTP using this link, I receive "Unknown file type: ftp://ftp.ncbi.nih.gov/snp/organisms/rat_10116/viewBatch/snpBatch_ENSEMBL_1050082.gz Check file extension"
Any help would be greatly appreciated, thank you.
IGV version: 2.3.25 (29)
Genome loaded: Rat (rn4)
