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.
Convert bams to vcf files
I have bam files downloaded from the 1000 Genomes Project and I need to have fasta files as the reference files (for -R option) in order to turn my bams into vcf files. Can you please tell me where to find fasta files from for my data? I tried using samtools and picard, but I don't really know where to get files to convert them to fasta..