We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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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.
Fasta Alternate Reference Maker Ignoring Insertions
I seem to be having an issue with the Fasta Alternate Reference Maker. Within my bam file and well as the vcf file there are notated insertions in 100% of the reads. When a fasta is created this insertion seems to be ignored. All of the noted deletions and mutations are carried over into the fasta file but insertions (1-3bp) seem to be ignored. I am looking at the bam files and vcf files on IGV so can see where individual mutations are.