AGELESSMolecularMicro

PAINT: Leishmania Sexual Reproductive Strategies As Resolved Through Compuational Methods Designed for Aneuploid Genomes

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Jahangheer S. Shaik, Deborah E. Dobson, David L. Sacks and Stephen M. Beverley

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AGELESS Package  

Example Data

Get Parental allele Frequencies

This page walks you though various steps required to generate file containing parental allele frequencies.

Prerequisites

1) Align the fastq files to the reference genome of interest using your favourite aligner (Bowtie, BWA, Novoalign etc.)
2) Sort the generated Binary alignment map (BAM) file using samtools 'sort' function
3) Generate an allele file using findAlleles utility of AGELESS
4) Generate an list file using listAlleles utility of AGELESS
5) Find parental SNVs using findSNPsSomy utility of AGELESS. Extract Homozygous SNVs from the parental lines and place them in a directory.
6) Generate a merged allele file using findAllelesSNPpositions utility of AGELESS.
7) Generate a merged allele frequency file using findAlleleFreqsSNPpositions utility of AGELESS.
8) Divide the merged allele file into individual files using DivideMergedFiles2ChrFiles utility of AGELESS.
9) Divide the merged allele frequency file into individual files using DivideMergedFiles2ChrFiles utility of AGELESS.

How to Run it?

Find parental allele frequencies using getParentAllelFrequencies utility of AGELESS. Type java -jar AGELESS.jar getParentAllelFrequencies -h for options.
  • -i is the directory containing individual allele frequency files generated using DivideMergedFiles2ChrFiles utility of AGELESS
  • -j is the directory containing individual allele files generated using DivideMergedFiles2ChrFiles utility of AGELESS
  • -k and -l are the parental file names from the merged allele file. 
  • -o is the directory containing parental allele frequencies

Command Example

java -jar AGELESS.jar getParentAllelFrequencies -i "..\DemoData\individualMergedAlleleFreqFiles" -j "..DemoData\individualMergedAlleleFiles" -k "FV1_SAT_srt.list" -l "LV39c5Hyg_srt.list" -o "..\DemoData\parentalAlleleFrequencies"

Output

The output of the DivideMergedFiles2ChrFiles program looks as follows:
parental allele frequencies
\