Test-drive the GATK tools and Best Practices pipelines on Terra
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Combine GVCF files problem
I used the following command to combine 3 VCF files which are outputs of HaplotypeCaller:
java -jar data/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \
-R data/ucsc.hg19.fasta \
-T CombineGVCFs \
--variant data/47V_post.ERC.vcf \
--variant data/48V_post.ERC.vcf \
--variant data/49V_post.ERC.vcf \
However, after combined all 3 files, in the output final VCF, I can only see ./. genotypes. What is the problem? how I can to fix this?