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.
HaplotypeCaller - AD missing in output vcf file
After I switched from the UnifiedGenotyper to HaplotypeCaller, I've noticed that the AD information is now missing from the output vcf file - everything else seems to be there.
I use the following command:
$GATK HaplotypeCaller \ -o $SAMPLE.haplo.vcf \ -I $SAMPLE.marked.realigned.recal.bam \ --dbsnp $DBSNP \ -stand_call_conf 30.0 \ -stand_emit_conf 10.0 \ -A DepthPerAlleleBySample \ -A BaseQualityRankSumTest \ -A DepthOfCoverage \ -A FisherStrand \ -A HaplotypeScore \ -A MappingQualityRankSumTest \ -A MappingQualityZero \ -A QualByDepth \ -A ReadPosRankSumTest \ -A RMSMappingQuality