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 (http://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq). 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 (ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/tomato_4081/VCF/). 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?
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gabriel.jabud •
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