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.
Ensembl GRCh38 indels and dsnp vcf files
I am using GATK3.8 to call variants in RNA-seq data. I am following the best practices for RNA-seq (https://software.broadinstitute.org/gatk/documentation/article.php?id=3891). My problem is during the indel realignment and base calibration steps. I have used the Ensembl GRCh38 genome version to map the reads. The indels and dsnp vcf files I can download from the resource bundle (hg38) have different chromosome notation and contig names (In my bam file chromosomes contain just number, ie "1", and in the vcf the format is "chr1"). Is there any indels and dsnp vcf files with the chromosome notation for Ensembl ? I can change the chromosome format in the vcf files but I dont know if this can be a problem in the next steps of the workflow.