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
