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Revision as of 14:58, 21 March 2013
, 14:58, 21 March 2013→BAM files
=== BAM files ===
=== BAM files ===
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls.
The BAM files need to be duplicate-marked and base-quality recalibrated in order to obtain high quality SNP calls. Generating these BAM files from original FASTQs is documented elsewhere as part of the [[Alignment Pipeline]] of gotCloud.
FASTQs can be converted to this type of BAM using the [[Alignment Pipeline]].
=== Index File ===
=== Index File ===
