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Visualizing Snp Data From Dbsnp In Igv
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6.0 years ago
axl058 • 0

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)

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