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

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

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PAINT Package

Example Data

Find Single nucleotide variations (SNVs) using a Reference Fasta File

This page walks you though various steps required to call Single nucleotide variations 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 an allele file using findAlleles utility of PAINT
4) Generate a list file using listAlleles utility of PAINT
5) Generate ploidy matrix using ConcatenatedPloidyMatrix utility of PAINT

How to Run it?

The findSNPsSomy utility of PAINT takes as input a list file, a reference fasta file and a chromosome somy file as inputs and generates a snv file.

-i is the list file is the file generated using listAlleles utility of PAINT.
-j is a reference fasta file
-l is the chromsome somy file that contains two columns. Column1 contains chromosome names and column 2 contains somies. The two columns are separated by a tab. See "..\DemoData\otherFiles\FV1Somies.txt" as an example. The somies can be determined by ConcatenatedPloidyMatrix utility of PAINT.

Command Example

java -jar PAINT.jar findSNPsSomy -i "..\DemoData\listFiles\LV39c5Hyg_srt.list" -j "..\DemoData\LmajorFriedlin6Trunc.fasta" -k "vcf" -m 25 -l "..\DemoData\otherFiles\LV39Somies.txt" -o "..\DemoData\snpFile\LV39c5Hyg_srt.vcf"

Output

The output is in standard VCF format. If -k is set to "tab", the output is in tabular format where some additional information is incorporated into the snv file. The headers are self explanatory.