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, 11:43, 15 October 2010
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− | This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. | + | 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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| == How to Run == | | == How to Run == |
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| + | This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information. |
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| + | (step 1) Site promotion using software glfMultiples [https://www.sph.umich.edu/csg/yli/GPT_Freq.011.source.tgz GPT_Freq]. |
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| == Important Filters == | | == Important Filters == |