need help

[Artur Kowalik]

Hi

I have tryied to upload the file generated from torrent server my PGM  (I could not sent this file because of volume restrictions) to use VAI but this message appeared
 "   Error File 'TSVC_variants_IonSet1_01.vcf' - Unrecognized format line 86 of custom track: chr1 81287388 . G C 49.46 PASS AO=5;DP=6;FAO=6;FDP=6;FR=.;FRO=0;FSAF=5;FSAR=1;FSRF=0;FSRR=0;FWDB=0.0280722;HRUN=2;LEN=1;MLLD=59.7327;RBI=0.127216;REFB=0;REVB=0.12408;RO=1;SAF=5;SAR=0;SRF=0;SRR=1;SSEN=0;SSEP=0;STB=0.5;SXB=0.37837;TYPE=snp;VARB=0.0494281;OID=.;OPOS=81287388;OREF=G;OALT=C;OMAPALT=C GT:GQ:DP:FDP:RO:FRO:AO:FAO:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:4.53373:6:6:1:0:5:6:0:5:0:1:1:5:0:0 (note: chrom names are case sensitive)"

what is wrong with my files?

Could you be so kind and explain me what is going on?

best wishes

Artur

 

**************************************

dr n. med. Artur Kowalik
Zak ad Diagnostyki Molekularnej
Swietokrzyskie Centrum Onkologii
ul. Artwinskiego 3; 25-734 Kielce
tel 41 367 42 59
fax 41 367 42 60

Artur Kowalik, PhD

Department of Molecular Diagnostics

Holycross Cancer Center

25-734 Kielce, Poland

St. S. Artwinskiego 3,

tel. +48 41 367-42-59

fax. +48 41 367-42-60

[Brian Lee]

Dear Artur,

Thank you for using the UCSC Genome Browser and your question about uploading a file generated from your Torrent Server Personal Genome Machine (PGM) System.

To submit your variant calls on our Variant Annotation Integrator, you must provide information in either the Personal Genome SNP (pgSnp) format or the Variant Call Format (VCF). While pgSnp-formatted variants may be uploaded as text in a Custom Track, VCF files are compressed and must be submitted with an indexed VCF file on a web server (HTTP, HTTPS or FTP), as well as being configured as a Custom Track (or if you happen to have a Track Hub, as hub tracks).

When a VCF file is compressed and indexed using tabix, and made web-accessible, the Genome Browser can fetch only the portions of the file necessary to provide annotated items in the VAI. This makes it possible to access variants from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC.

Please see this page about VCF format for details, http://genome.ucsc.edu/goldenPath/help/vcf.html.

By following the VCF custom track workflow, you can construct a custom track with a line like: track type=vcfTabix name="My VCF" bigDataUrl=http://myorg.edu/mylab/my.vcf.gz. Please note, that in addition to the VCF file at http://myorg.edu/mylab/my.vcf.gz, the associated index file, http://myorg.edu/mylab/my.vcf.gz.tbi, must also be available at the same (example) location.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have further questions, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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