Hi, I want to add a custom track containing information from a vcf file downloaded from the Exome Variant Server (http://evs.gs.washington.edu/EVS/). I've downloaded the file in bgzip format and indexed it using tabix, according to instruction on the VCF help page from Genome browser (http://genome.ucsc.edu/goldenPath/help/vcf.html).
Then I've opened the add Custom Track page in Genome Browser and did as following: 1. I've clicked on "Choose file" button and selected the file from my computer 2. In the text box I've added this custom track definition track type=vcfTabix name="NEU1_EVS" bigDataUrl=http://myorg.edu/mylab/EVS_SNP_NEU1.vcf.gz description="NEU1 variants from EVS project" visibility=pack db=hg19 chromosomes=chr6 However the system use to show this error: Error File 'EVS_SNP_NEU1.vcf.gz' - Unrecognized format line 31 of somefile.gz: 6 31827505 rs114618932 C T . PASS DBSNP=dbSNP_132;EA_AC=0,4488;AA_AC=7,3027;TAC=7,7515;MAF=0.0,0.2307,0.0931;GTS=TT,TC,CC;EA_GTC=0,0,2244;AA_GTC=1,5,1511;GTC=1,5,3755;DP=121;GL=NEU1;CP=0.0060;CG=-3.45;AA=C;CA=unknown;EXOME_CHIP=no;GM=NM_000434.3;FG=coding-synonymous;AAC=none;PP=413/416;CDP=1239;GS=NA;PH=unknown (note: chrom names are case sensitive) I guess that it would be something wrong in the upload process or custom track definition, since I obtain the same error using data and track definition from Genome Browser tutorial example (Example Two from the help page http://genome.ucsc.edu/goldenPath/help/vcf.html). Any suggestion? Thanks! Edoardo Giacopuzzi, Ph.D. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
