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Old 02-17-2012, 11:02 AM   #1
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Default Merging bam files

According to best practice variant detection if You have multiple sequencing of the same sample from 2 different runs You need to merge bam files prior to realigner/indel realigner/mark duplicates. Is it possible to merge bam files that were already realigned/marked duplicated (per each bam separately) ?

Last edited by memento; 02-17-2012 at 11:21 AM.
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Old 02-17-2012, 03:39 PM   #2
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Realignment is performed on a set of reads. If you merge two BAMs and add reads to a locus then realignment is needed. Same goes for marking duplicates or recalibrating bases.

Last edited by adaptivegenome; 02-17-2012 at 03:39 PM. Reason: typo
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