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POPSICLE- a software suite to determine population structure and to establish genotype-phenotype associations using Next-generation sequencing data |  |
MAIN INDEX ANALYTICAL PIPELINE CONTACT SYSTEM REQUIREMENTS POPSICLE Package Download Manual pages in HTML format Used Case |
SampleBaseLineFile Prerequisites
It samples the baseline file to include a subset of markers from the original file. How to run it? java -jar LPDtools.jar SampleBaseLineFile -i popsicleBaselineFile -o outputSampledBaselineFile -m 2 Here, -i is the baseline file generated using the utility FindDivergenceFromBaseline . -o is the sampled version of the file. -m is the factor that determines the number of markers that are to be retained per kb. If -m 2, then 2 markers every kb Output Output is the same format as the output from the utility FindDivergenceFromBaseline. Except that the generated file is the sampled version of the original file. |
| CITATION: Jahangheer S. Shaik, Asis Khan and Michael E. Grigg, "POPSICLE: A Software Suite to Study Population Structure and Ancestral Determinants of Phenotypes using Whole genome Sequencing Data", submitted to PLoS special edition |