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

 FindAlleles
Prerequisites
Align the reads to the genome and sort them by genomic position using tools such as samtools. See here for details.
What does it do?
Finds the nucleotide composition at  positions where there are reads aligned to the genome
How to run it?
java -jar LPDtools.jar findAlleles -i directoryBAMfiles -n 1 -o outputDirectoryAlleleFiles
Here, -i is the directory where sorted aligned Binary Alignment map files are placed. -o is the output directory containing the allele files. -n is the bp window. -n 1 finds allele composition at each base
Output
The output directory contains the allele files that look as follows:
findAllelesOP

The chromosome name is listed first followed by other information corresponding to that chromosome.
For example:
  • 28      0;0;9;0;9;0;2295- provides information regarding base position 28 on chromosome Pf3D7_01_v3
  • 28      0;0;9;0;9;0;2295- Indicates allele composition is 0 As, 0 Ts, 9 Cs and 0 Gs. This locus is homozygous for 'C' with 100% allele frequency.
  • 28      0;0;9;0;9;0;2295- Provides information regarding the orientation of the reads. In this case, there are 9 reads with forward orientation and 0 with reverse orientation that contribute to the allele information
  • 28      0;0;9;0;9;0;2295- Indicates cumulative mapping quality of the reads

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