Question: Genotyping small variants
gravatar for Manuel
3.6 years ago by
Manuel370 wrote:
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? Thanks!
genotyping • 812 views
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