Hi Edoardo, We suggest that you skip this step:
1. I've clicked on "Choose file" button and selected the file from my computer The file will be accessed from the URL in the custom track definition so no uploading is necessary. If you have further questions, please write to the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Edoardo Giacopuzzi <[email protected]> Date: Tue, Dec 20, 2011 at 7:16 AM Subject: [Genome] Adding custom track in vcf format To: [email protected] 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
