Perform realignment around indels before detecting MSI on BAM files?Answered
I have a set of pre-processed (duplicates marked and BQSR performed) BAM files deriving from gene-panel sequencing data. I know that realignment around indels is kind of outdated nowadays since the variant caller does this intrinsically (GATK v4.2.0). However, I wish to perform an MSI-analysis on these samples using a software outside GATK. Would you recommend me to perform realignment around indels before running this type of analysis? Or is BQSR suffice in regards of pre-processing for most downstream analysis of BAM-files that does not incorporate variant claling?
Hi David Lord,
Thanks for your question. We aren't able to provide a definitive answer because this isn't quite in our scope.
We would recommend reaching out to the team that makes the MSI-analysis software to see what pre-processing steps they recommend. If they recommend indel realignment, you could go back to GATK3 and use the indel realignment tool in that package. Like you said, the reason we don't have a stand alone tool for indel realignment is because our variant callers perform indel realignment within the tools.
Hi David Lord,
I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
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