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

 FindDivergenceFromBaseline
Prerequisites
  1. Find somies using findSomies utility of POPSICLE
  2. Find alleles using findAlleles utility of POPSICLE
  3. Generate Popsicle input file using the utility GenerateInputFromAlleleFiles or alternately use the filtered files generated using the utility RemoveInsignificantLoci or RemoveLociWithLotsOfMissingData
What does it do?
It finds how much each sample deviates from the reference
How to run it?
java -jar LPDtools.jar It  -i inputPopsicleFile -o outputPopsicleBaselineFile
Here -i is the input POPSICLE file generated using the utility GenerateInputFromAlleleFiles or using the utility RemoveInsignificantLoci or RemoveLociWithLotsOfMissingData. -o is the output file.
Output
popsiclebaseline
The allele composition at each base position is compared against the reference and scored based on the deviation. The missing data is represented by a "-". A value of 0 would mean concordance with the reference.

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