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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 |
Generate necessary files to draw circos plots Prerequisites
It generates files required to draw circos plots How to run it? java -jar LPDtools.jar ConvertPopsicle2CircosHighlights -i polishedArrangedAncestryFile -o outputDirectory -j PopsicleBaselineFile -k clustersFile Here, -i is the ancestry file generated using the utility POPSICLEIntermediate , polished using the utility PolishPopsicle and arranged using the utility ArrangePopsicleByClustersFormed. -k is the clusters file generated using the utility PerformKmeansClustering and -j is the baseline file generated using the utility FindDivergenceFromBaseline utility of POPSICLE Output  Outer concentric circle is local ancestries, middle concentric circle is global ancestries and inner concentric circle is clade assignment of the sample. Links demonstrate similarities between the clades |
| 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 |