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.
Unified Genotyper Emit all sites
I am calling variants in the mitochondrial genome using the following command from a bash script:
java -Xmx1g -jar $GATKjar -R $REF -T UnifiedGenotyper -ploidy 1 -I $BAM -o $OUT --output_mode EMIT_ALL_SITES
Across 300 genomes it consistently does not call anything at position 3107 of the genome. I have checked the Bam files and made sure that there is coverage at that position. I have not been able to find anyone else who has encountered this problem on the forum. I was wondering if there is something wrong with how I am calling variants?