I have small somatic variants in a vcf file. I now want to genotype them in another Bam file. What are tools for this task?
My background is that I have somatic variants from mutect and scalpel and now want to see if they are in other samples as well. For snvs I can have successfully created a bed file from the regions and then used samtools mpileup. Indels might be trickier due to ambiguities in particular in cancer samples.
What would be your approach here?