Hello, We are still working on support for VCF custom tracks, but I can explain a little bit about the error you pasted below.
I can generate the same error if I paste the Sanger ftp link directly into the "Paste URLs or data:" box on the custom tracks page. However, vcf+tabix files, like bigBed and bigWig, need to have a special track line pasted into that box that looks something like this: track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gz I tried that with your URL and got a bunch of different errors. One of our engineers guessed that the new errors might be because the file is using an older version of vcf (3.3) and the Genome Browser needs 4.0 or higher. (But this is just a guess.) Regarding your question about the example tracks referenced in the text on our test server (http://genome-test.cse.ucsc.edu/goldenPath/help/vcf.html), it doesn't work because the file it is referencing is not on our production machine (at genome.ucsc.edu) yet. If you change the URL in the example from: http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz to http://genome-test.cse.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz You should be able to successfully load the example. I hope this helps. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/26/11 4:13 PM, Yi Mao wrote: > I am trying to add custom track from the UCSC web site using the vcf > input format. > I have tried several inputs in .vcf files including 1000 genome snp data. > When I > uploaded these snp files into the UCSC genome browser, and always got > an error message as follows: > > Error Unrecognized format line 12 of > ftp://ftp-mouse.sanger.ac.uk/current_snps/20111102-snps-all.vcf.gz: 1 > 3000054 . C T -1 . AC=2;AN=34 GT:ATG:MQ:HCG:GQ:DP 0/0:0:59:-1:109:24 > 0/0:0:59:-1:82:15 0/0:0:60:-1:52:5 0/0:0:60:-1:133:32 0/0:0:60:-1:52:5 > 0/0:0:59:-1:85:16 0/0:0:60:-1:94:19 0/0:0:60:-1:61:8 0/0:0:60:-1:82:15 > 0/0:0:60:-1:73:12 0/0:0:59:-1:88:17 0/0:0:57:-1:57:15 > 0/0:0:52:-1:94:25 0/0:0:59:-1:106:23 0/0:0:59:-1:79:14 > 1/1:1:56:1:73:12 0/0:0:60:-1:79:14 (note: chrom names are case > sensitive) > > The input format I am using is > 1 3000054 . C T -1 . AC=2;AN=34 > GT:ATG:MQ:HCG:GQ:DP 0/0:0:59:-1:109:24 0/0:0:59:-1:82:15 > 0/0:0:60:-1:52:5 0/0:0:60:-1:133:32 0/0:0:60:-1:52:5 > 0/0:0:59:-1:85:16 0/0:0:60:-1:94:19 0/0:0:60:-1:61:8 > 0/0:0:60:-1:82:15 0/0:0:60:-1:73:12 0/0:0:59:-1:88:17 > 0/0:0:57:-1:57:15 0/0:0:52:-1:94:25 > 0/0:0:59:-1:106:23 0/0:0:59:-1:79:14 1/1:1:56:1:73:12 > 0/0:0:60:-1:79:14 > > In the meantime, I also attempted to repeat some examples for vcf > format listed below > http://hgwdev.cse.ucsc.edu/goldenPath/help/vcf.html > so far, no success. > > Any help is greatly appreciated. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
