Test-drive the GATK tools and Best Practices pipelines on Terra
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GenotypeGVCFs problem with rsID
I run the following command for "GenotypeGVCFs" for 3 VCF files output of HaplotypeCaller as below:
java data/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \
-R data/ucsc.hg19.fasta \
-T GenotypeGVCFs \
--variant data/47V_post.ERC.vcf \
--variant data/48V_post.ERC.vcf \
--variant data/49V_post.ERC.vcf \
but in a final VCF output there is no rsID information and all rows are "."
what is the problem? I am really confused. Could you please advise how to get SNP-ID in the output VCF