Hi, I'm new at this and trying to construct a sequence validation pipeline.
I'm using this command to call variants in my script:
bcftools mpileup -f "$1" "$2" | bcftools call -mv -Ob -o temp_variants.bcf
When calling bam files with a double deletion, it is able to detect the variant. However, when there is only a single deletion in the bam file, the variant file is empty?
Any ideas/help would be much appreciated!