https://www.walmart.com/ip/Popsicle-Rainbow-Big-Stick-3-5-oz/198225061 POPSICLE- a software suite to determine population structure and to establish genotype-phenotype associations using Next-generation sequencing data niaidlogo





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POPSICLE Package  

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Used Case

 RemoveInsignificantLoci
Prerequisites
  1. Find somies using findSomies utility of POPSICLE
  2. Find alleles using findAlleles utility of POPSICLE
  3. Generate popsicle input using GenerateInputFromAlleleFiles utility of POPSICLE. Alternately, you can use the file generated using the utility RemoveLociWithLotsOfMissingData
What does it do?
It removes the markers that dont vary much across the samples.
How to run it?
java -jar LPDtools.jar  RemoveInsignificantLoci -i popsicleInputFile -o OutputFilteredPopsicleFile1.txt -m 0.9

Here, -i is the POPSICLE input file generated using the utility GenerateInputFromAlleleFiles utility of POPSICLE pipeline. -o is the filtered output file after removing markers that dont pass the filter. -m is the factor that determines which markers are filtered out. If -m is set to 0.8 and if a marker has 80% of the samples have the same allele, it is filtered out. 
Output
The output is the same format as that of the utility GenerateInputFromAlleleFiles

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