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.
which input files for IndelRealigner and BaseRecalibrator?
For input file of known indels in IndelRealigner, I would like to ask what is the pros and cons for using Mills_and_1000G_gold_standard.indels.b37.vcf vs 1000G_phase1.indels.b37.vcf ? Both are available from the resource bundle.
A similar question is which of the above 2 files would you suggest for input for known Indel sites in the BaseRecalibrator? Is it the Mills_and_1000G_gold_standard.indels.b37.vcf as the workflow use gold.standard.indel.vcf?
Which should I choose between dbsnp_138.b37.vcf and 1000G_phase1.snps.high_confidence.b37.vcf for the other known site inputs? Is it dbsnp_138.b37.vcf that contains more variant?