Question: VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
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gravatar for Ana
7 months ago by
Ana140
Ana140 wrote:

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-4.0.4.0/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

gatk • 461 views
ADD COMMENTlink modified 7 months ago by finswimmer11k • written 7 months ago by Ana140

Hello,

were there any warning/error messages? Could you post some examples from the vcf file from variants that are missing in the result?

Thanks.

fin swimmer

ADD REPLYlink written 7 months ago by finswimmer11k

No, I did not get any error message. I just get only 1 million SNPs in the table and I do not know which of them from the main vcf file

ADD REPLYlink written 7 months ago by Ana140
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