I'm trying to take a merged vcf file and output counts of homo/het to a table using Variants to Table. the tables are not anyway the same length as the vcfs that I am creating them from. Is there any reason why the VariantstoTable walker would be removing data? I can go in and look at the vcf file and find snps that have het genotypes that are not included in the output table. any ideas? my code is below.
java -jar ~/resources/GenomeAnalysisTK.jar -R ~/resources/genomes/ucsc.hg19.fasta -T VariantsToTable -V test.vcf -F CHROM -F POS -F HET -F HOM-REF -F HOM-VAR -o test.table`