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The variant which is seen single sample gvcf is missing after combing multiple samples
@Sheila, I generally use the following command to combine gvcf of my samples. when new sample comes I keep adding them to already combined gvcfs
java -Xmx20g -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T CombineGVCFs -R /mnt/exome/ReferenceFiles/human_g1k_v37.fasta -V Combined_200.gvcf -V samplea.gvcf -V sampleb.gvcf -V samplec.gvcf -o $outname.gvcf
But one of the variant which is seen in gvcf of a single sample is not seen in combined gvcf. Please help me to rectify the issue.
Thanks and Regards