Question: Genotyping small variants
0
gravatar for Manuel
4.0 years ago by
Manuel370
Germany
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 • 879 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Manuel370
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1794 users visited in the last hour