mkatari-bioinformatics-august-2013-gatknotes
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| mkatari-bioinformatics-august-2013-gatknotes [2014/06/13 08:28] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatari | ||
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| - | Now we merge the bam files and then sort and index them | + | In some cases there may be a need to clean the sam/bam file(s) (soft-trimming the coordinates). To do this use CleanSam in Picard tools. You may want to just do it to all to avoid the error in a workflow, but it may not be necessary. |
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| - | java -jar / | + | java -jar / |
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| + | Now we merge the bam files and then sort and index them. If you cleaned the bam file, remember to use the cleaned ones. | ||
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| + | java -jar / | ||
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| - | Finall | + | Finally |
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mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari