I'm building a variant calling pipeline for mouse using GATK and I wanted to know if there are any indel databases other than dbSNP that can be used in the "--known" option while preparing intervals for the local realignment step.
If I instead just run this step without any known databases, any ideas on how it might effect the accuracy or computational time of the subsequent variant calling steps?
Any input is appreciated.
If I instead just run this step without any known databases, any ideas on how it might effect the accuracy or computational time of the subsequent variant calling steps?
Any input is appreciated.