UnifiedGenotyper- Can it be used to call SNP's in bacterial genomes

schangayil2001

UnifiedGenotyper- Can it be used to call SNP's in bacterial genomes

Mark_DePristo

Yes

schangayil2001

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?

Thanks!

Geraldine_VdAuwera

Hi there, please have a look at the quality control and simple analysis tools in the technical documentation.

aadhyadi

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? Thanks

Geraldine_VdAuwera

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.