This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
RealignerTargetCreator with reduced representation libraries
My bam files contain reads from a reduced representation library where the genomic DNA was digested with restriction enzymes--so every paired-end read starts with a restriction site. Will this affect how GATK discovers regions that require realignment, or the effectiveness of the realignment itself?