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combing or merging vcf
i need to seek your advice in combining vcf files using combinevariants
i have six samples and i did variant calling separately using unified genotyper.
i need to know can i use this command by specifying --variant six times for each vcf and can get ALL variants in all six files
i dont want unique or common even if they have some common. this -genotypeMergeOptions UNIQUIFY is confusing
java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T CombineVariants \
--variant input1.vcf \
--variant input2.vcf \
-o output.vcf \
i want to create mutli-sample vcf file like the one in 1000genomes