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?