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merge multi-sample bam files
I have with me 1000 samples that were pooled together in 5 different libraries and sequenced for genomic regions. So first, for each library, I independantly performed alignment, marked duplicates,realigned the bam files and also did recalibration and separated the bam file for each individual. Now I have 1000 individual bam files and I wanted to check the target coverage and perform variant calling.
I wanted to know if it makes sense to merge the bam files according to cases:controls and perform the analysis with 2 bam files or is it better to carry on with single individual bam files ?