POPSICLE- a software suite to determine population structure and to establish genotype-phenotype associations using Next-generation sequencing data

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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? This utility finds the somies of the samples based on the cluster assignments. How to run it? Run the utility as follows: java -jar LPDtools.jar FindSomies -i directoryBAMfiles -o outputSomies.txt -m 1 -k chrSizes.txt Here, -i is the directory where sorted aligned bam files are placed.  -m is the ploidy of the organism. For haploid organism, set m to 1, for diploid, set m to 2 -k is the file with chromosome sizes. Column 1 contains chromosome names and column 2 contains the size of the chromosome. See below for an example. The reads aligned to each chromosome are dependent on the somy of the chomosome and the size of the chromosome. Higher the somy, more reads are aligned to the chromosome. Bigger the chromosome, more reads are aligned to the chromosome. The reads aligned to each chromosome are normalized by the chromsosome sizes. The average value of these normalized values correspond to the ploidy of the organism. Accordingly, the normalized values are scaled and the somies are reported. Output Here, each column is a sample and each row is a chromosome. Each block is therefore, somy of a chromosome in a sample.