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, 20:35, 17 November 2010
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| This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [mailto:yunli@med.unc.edu Yun Li] for the 1000 Genomes Low Coverage Pilot Project. | | This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [mailto:yunli@med.unc.edu Yun Li] for the 1000 Genomes Low Coverage Pilot Project. |
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− | == Input Data == | + | >== Input Data == |
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| To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. Sample files are available at [ftp://share.sph.umich.edu/1000genomes/pilot1/examples/glf.tgz sample glf files]. | | To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. Sample files are available at [ftp://share.sph.umich.edu/1000genomes/pilot1/examples/glf.tgz sample glf files]. |
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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: | | 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 | + | samtools pileup -g -T 1 -f ref.fa my.bam > my.glf |
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− | Note: you will need the reference fasta file ref.fa to create glf file from bam file. | + | Note: you will need the reference fasta file ref.fa to create glf file from bam file. |
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| == How to Run == | | == How to Run == |