AGELESSMolecularMicro

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

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




MAIN

INDEX

ANALYTICAL PIPELINE

CONTACT

SYSTEM REQUIREMENTS

PAINT Package  

Example Data

Generate A merged Allele Frequency file

This page walks you though various steps required to generate a Merged allele frequency file using PAINT package.

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 allele files using findAlleles utility of PAINT
4) Generate list files using listAlleles utility of PAINT
5) Find parental SNVs using findSNPsSomy utility of PAINT. Extract Homozygous SNVs from the parental lines and place them in a directory.

How to Run it?

The findAlleleFreqsSNPpositions utility of PAINT package takes the parental homozygous SNV files and finds markers where parental lines are different from each other. It then finds the frequency composition of alleles from all files in the listFiles directory at those markers. Type java -jar PAINT.jar findAlleleFreqsSNPpositions -h for options.
  •  -i is the directory where the list files are placed. List files are generated by  listAlleles utility of PAINT.
  • -j is the directory where parental homozygous SNVs are placed. The SNVs are found using the findSNPsSomy utility of PAINT. Alternatively, you may use any of your favourite SNV callers.
  • -k is either "vcf" or "tab". If the generated SNV file is in VCF format then set -k to "vcf" or "tab" otherwise
  • -o is the output merged allele frequency file

Command Example

java -jar PAINT.jar findAlleleFreqsSNPpositions -i "../DemoData/listFiles" -j "../DemoData/snpFile/homozygous/" -o "../DemoData/otherFiles/mergedAlleleFreqencies.txt" -k "vcf"

Output

The output of the findAllelesSNPpositions utility program looks as follows:
merged allele frequencies
Markers are the genomic positions where both parental lines are different from each other.  The subsequent columns contain the allele frequency composition of the files in the listFiles directory (-i option in findAllelesSNPpositions). FV1_SAT and LV39c5HYG are the parental lines and as can be seen, both the parental lines are homozygous and therefore the allele frequencies are close to 100%. The hybrids  as expected have contribution from both the parental lines and therefore are heterozygous. The allele frequencies of alleles in the hybrids are listed separated by ":". Missing data is represented by "-". The users can filter out the markers where parental lines have missing data (LmjF.01 position 20 in FV1_SAT for example). This can be done by "filter" option in excel. Perform filtering in both merged allele and merged allele frequency files if filtering is to be performed.