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

 RemoveLociWithLotsOfMissingData
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 by using the utility RemoveInsignificantLoci
What does it do?
It removes the markers with lots of missing data.
How to run it?
java -jar LPDtools.jar RemoveLociWithLotsOfMissingData -i popsicleInputFile -o outputFilteredPopsicleFile -m 0.1
Here -i is the popsicle input file generated using the utility  GenerateInputFromAlleleFiles or filtered popsicle file generated using the utility RemoveInsignificantLoci. -o is the output file generated after removing markers with lots of missing data. -m is the maximum missing data tolerable. Eg. if -m is set to 0.7, markers with 70% or more missing data are ignored.
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