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02-17-2012, 11:02 AM
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#1 |
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Member
Location: UK Join Date: Nov 2010
Posts: 49
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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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02-17-2012, 03:39 PM
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#2 |
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Super Moderator
Location: US Join Date: Nov 2009
Posts: 437
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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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