It looks like you're new here. If you want to get involved, click one of these buttons!
UnifiedGenotyper- Can it be used to call SNP's in bacterial genomes
Mark A. DePristo, Ph.D.
Co-Director, Medical and Population Genetics
Broad Institute of MIT and Harvard
Thanks for the prompt answer. As your answer was yes, I would like to know whether we can find the coverage at each position irrespective of whether there is SNP or not in that position. If yes, which java class in the API does it. Do you also have Javadocs for all your APIs?
Hi there, please have a look at the quality control and simple analysis tools in the technical documentation.
Geraldine Van der Auwera, PhD
Hi there, what kind of filters should one use for applying filters on variants called in bacterial genomes? Do you have recommendations for the same?
We recommend that you apply the Best Practices as described in the documentation. The main adjustment you will need to do is to choose or generate an appropriate set of known variants as described previously in the docs and on the forum.