Question: Complete Genomic Vcf File Visualization
0
gravatar for kanwarjag
6.3 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

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.

vcf • 2.8k views
ADD COMMENTlink modified 6.3 years ago by hannes.svardal180 • written 6.3 years ago by kanwarjag1.0k
1
gravatar for hannes.svardal
6.3 years ago by
Austria
hannes.svardal180 wrote:

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/

ADD COMMENTlink written 6.3 years ago by hannes.svardal180
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