I recently used GATK, the latest version to carry out Indel realignment for my bam files. I have read at few places that one needs to fix the mate position information as the reads mapping position may change during realignment. My question is that does this step is taken care of y GATK automatically or one needs to run Picard fixmates before going for subsequent analysis.
Dear Community and GATK's team,
I have one question about the cleaning step before SNP calling, mainly about local realignment around indels.
I read on some website describing their workflow that alignments may change during the realignment process, it would prefer to fix the mate information and Picard offers this utility to do that for us. is it true? Or are there only any insert sizes that can change? If there are some change of insert sizes, is there a tool that checks that these changes are ok?
What do you use Picard's tool, FixMateInformation.jar, to fix the mate information when using paired-end data ?
Up to now, I have not used in my pipeline. Maybe this is a mistake. If we have to add this step, should we add this step after the realignment step or recalibration step?
Thank you for your help,