Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

SNPs Call using HaplotypeCaller

I am using the following script to call-variants from RNAseq data using HaplotypeCaller. However, in the VCF output I only have 0/1 and 1/1 genotype and there is no 0/0 genotype. How I can get all 3 class of genotype in the output? please advise. Thanks

java -jar /home/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar \
-R /home/ucsc.hg19/ucsc.hg19.fasta \
-T HaplotypeCaller \
-I /home/sample1.bam \
-recoverDanglingHeads \
-dontUseSoftClippedBases \
-stand_call_conf 20.0 -stand_emit_conf 20.0 \
--dbsnp /home/dbsnp_137.hg19.vcf \
--output_mode EMIT_ALL_SITES \
--genotyping_mode DISCOVERY \
--out /home/output.vcf

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