Hello, Francesco. Unfortunately, there is currently no way to configure the display of additional options. For VCF files that don't have multiple genotypes, we internally downconvert to a simpler format that has no names or tags, just variants and counts.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Lescai, Francesco Sent: Tuesday, June 19, 2012 7:16 AM To: [email protected] Subject: [Genome] Fwd: VCF custom tracks empty My apologies, it works now. I just hadn't the latest version of tabix installed. followed again the instruction, everything works. I just have one additional question: when roll over the variant with the mouse, in your multisample VCF file (visibility=pack) I can see a yellow box popping up with name and additional features. in mine, which is single sample, I can only see the allele numbers. is there any way to configure what information should appear when rolling over the variant with the mouse? thanks, Francesco Begin forwarded message: From: "Lescai, Francesco" <[email protected]<mailto:[email protected]>> Subject: VCF custom tracks empty Date: 19 June 2012 12:40:20 GMT+01:00 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Hi there, I tried to follow precisely the instructions in http://genome.ucsc.edu/goldenPath/help/vcf.html but my tracks are always empty. I thought it might be the missing "chr" but then I saw your example file is on ENSEMBL format, i.e. without "chr" http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz I was trying to pass single sample VCFs while the example is multi-sample, so I tried a multi-sample one but the browser was empty again. My file are bgzipped and indexed with tabix, I don't receive any error message. I checked with a zcat the file to contain data. They have been generated with GATK, and the file format is v4.1 which I understand should be supported. the track line I'm using is track type=vcfTabix name=PE1Variants db=hg19 visibility=pack maxWindowToDraw=200000 bigDataUrl=https://myurl/P E1/PE1.noref.vcf.ucsc.vcf.gz I'm attaching here one of these files. Any clue of what I must be missing? thanks for your help, Francesco ---------------------------------------------------------------------------- ----- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development & Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: [email protected]<mailto:[email protected]> phone: +44.(0)207.905.2274 [ext: 2274] ---------------------------------------------------------------------------- ---- ---------------------------------------------------------------------------- ----- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development & Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: [email protected]<mailto:[email protected]> phone: +44.(0)207.905.2274 [ext: 2274] ---------------------------------------------------------------------------- ---- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
