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BQSR with MuTect2: use it or not ?
I've been reading some threads on the forum about BQSR with MuTect2. I know it has been proposed in Best-Practices uses. However, there were a lot of mixed comments and I can't find a clear conclusion on whether to use BQSR with MuTect2 since MuTect2 takes into consideration the base quality score, and that's what BQSR does. I am working on 18 human samples matched normal and tumor. Those samples have been exome-sequenced. I am using MuTect2 from GATK 3.7 stable version. I generated results using the proposed pipeline here. I used the following inputs:
Following this thread here for example, I am worried that potential true variants could be altered due to recalibration.
I also have another doubt, in BQSR thread, I just want to make sure that BQSR does NOT change the base of the variant itself but it just assigns a low base quality score if it gets recalibrated.
I have analyzed commands ran by The Cancer Genome Atlas and they actually use BQSR in their workflow. So finally, I would like to know if it safe to use BQSR with MuTect2 ? It is better to have multiple dbSNPs to avoid having mismatches of potential variants (for example, I have downloaded from NCBI all kwown SNPs of the human ~ 57GB vcf file) ?
Thank you in advance !