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, 12:32, 15 October 2010
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| == Input Data == | | == Input Data == |
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− | To get started, you will need bam files in the standard format [http://samtools.sourceforge.net/SAM1.pdf bam format]. | + | To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. |
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| + | If you do not have glf files, you can generate them from bam files (bam format also specified in [http://samtools.sourceforge.net/SAM1.pdf glf format bam format]) using the following command line: |
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| + | samtools pileup -g -T 1 -f ref.fa my.bam > my.glf |
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| == How to Run == | | == How to Run == |
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| == Important Filters == | | == Important Filters == |