Question: Are there any "complete" VCF files for tomato available?
gravatar for gabriel.jabud
6.5 years ago by
United States
gabriel.jabud40 wrote:

I'm following the GATK pipeline for variant calling of tomato whole genome data I am analyzing and am stuck on the base recalibration step (  It requires me to use a VCF file containing known variant sites.  The only VCF file I've found so far is the one on NCBI's dbSNP database (  However the combined VCF file for all 12 chromosomes is only about 237 lines long including the header, so I doubt it will help to recalibrate with such a small amount of known variants.

Should I just go ahead and skip the recalibration step or is there a more complete VCF file containing variants of tomato?

gatk solanum variants tomato vcf • 2.0k views
ADD COMMENTlink written 6.5 years ago by gabriel.jabud40

You'll likely need to bootstrap.

ADD REPLYlink written 6.5 years ago by Devon Ryan98k
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