Complete Genomic Vcf File Visualization

Question

[kanwarjag]

I wonder how best I can visualize whole genome data of complete genomics. I tried to use VCF file but when I try to index it gives an error messages
It says - The provided VCF is malformed appx line 32: The VCF does not allow for white space in th eINFO field. Offending field value was DBSNP =6678138; SIFT_Function=tolerated------. When I manually removed this particular entry then it complains We never saw the reuired CHROM header line (starting with #) for the input VCF file.

Any suggestion or alternate of VCF visualization for complete genomics.

Answer 1

[hannes.svardal]

How was the VCF created? The file is apparently badly formated. I recommend that you use the same tool for creating the file and indexing. Use recent versions. GATK is pretty reliable.

For viewing the VCF, I recommend igv viewer: http://www.broadinstitute.org/igv/