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.pl script (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?