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Test-drive the GATK tools and Best Practices pipelines on Terra
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I am using the VariantsToTable walker to convert my vcfs to tabular format. Previously I have done same filtering with vcftools in my vcfs input files. VariantsToTable walker output file only contains just a few of the SNPs I have in my input file. Specifically, those which have the tag "PASS" in FILTER column. I need a table with all the input SNPs, regardless FILTER column value. Is there any way to do it?