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.

A Variant which is supported by 21 reads in IGV is not called by HaplotypeCaller...

Below command is used for the purpose
java -jar /mnt/exome/Softwares/GenomeAnalysisTK.jar -T HaplotypeCaller -R hg19.fa -I 62352575_S28_realigned.bam -L nexterarapidcapture_exome_target_region.bed --genotyping_mode DISCOVERY -o new.vcf

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