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Realigning sample-merged bam files?

jschoenejschoene Roslin InstituteMember

Following GATK's best practices, I have individually realigned/recalibrated my sample-lane bams and merged them by sample:

sample1_lane1.dedup.realn.recal.bam -->
sample1_lane2.dedup.realn.recal.bam --> sample1.merged.bam
sample2_lane1.dedup.realn.recal.bam -->
sample2_lane2.dedup.realn.recal.bam --> sample2.merged.bam
...

I am ready to dedup and realign my sample merged bams, however I am uncertain on the best approach. Is the consensus to convert back to fastq via Picard (MarkDuplicates, SortSam, and SamToFastq) and then run bwa mem? Or is it more expedient/accurate to realign the sample-merged bam using bwa aln followed by bwa sampe?

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