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.
DiagnoseTargets: annotating output VCF file with gene names
Hi GATK !
I am using DiagnoseTargets on exome data with the 1000 Genomes human v37 ref genome and Illumina exome interval .bed file.
It seems that DiagnoseTargets (unlike DepthOfCoverage) doesn't accept the -genelist argument.
1) What would be a possible alternative to add the gene name on the output interval stat .vcf file (and optionally the --missing intervals)?
Is VariantAnnotator (with the --comp argument) would work?
2) What annotation file should I use?
sortByRef.plscript (mentioned here) not being available anymore, did it only (i) discard records with non-Chr1-22/X/Y/M, and (ii) sort by Chr?
Does VariantAnnotator automatically adjust from zero-based half-open intervals (UCSC standard) to one-based closed intervals or should I modify the file during the previous steps as well?