VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
I am trying to convert my vcf file to a flat tab-separated format by using "VariantsToTable" in GATK. I am particularly interested in DP at the sample annotation for my analysis. I am using
/data/programs/gatk-188.8.131.52/gatk VariantsToTable -V final.vcf -GF DP -O snps.DP.tab
My vcf file consists of over 4 million SNPs, but the table that I get from running VariantsToTable consists only nearly 1 million SNPs. I wonder what is wrong!
Does anyone knows how can I sort this out. Thanks
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