PopDep - PlantGeneticsLab/TIGER GitHub Wiki
Overview
PopDep performs read depth profiling of a population, based on whole-genome shotgun (WGS) sequencing data. It is useful to identify conserved/single-copy/well-assembled region from a reference genome. It outputs 2 statistics,
- Mean depth of all taxa at a specific site
- SD of depth of all taxa at a specific site
Prerequisites
Java 8
http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html
Samtools
http://samtools.sourceforge.net/
Usage
The commandline example of PopDep is
- java -Xmx100g -jar TIGER.jar -a PopDep -p parameter_popdep.txt > log.txt &
The content of the parameter file is as follows.
#App: PopDep
#Author: Fei Lu
#Email: [email protected]; [email protected]
#Homepage: https://plantgeneticslab.github.io/home/
#PopDep is used to perform perform depth profiling in a population, based on media/high depth (e.g. >5X) whole genome sequencing data. They are useful to identify conserved regions of a genome.
#It outputs 2 statistics,
#Mean depth of all taxa at a specific site
#SD of depth of all taxa
#To run and pipeline, the machine should have both Java 8 and samtools installed. The lib directory should stay with TIGER.jar in the same folder.
#Command line example is as follows,
#java -Xmx100g -jar TIGER.jar -a PopDep -p parameter_popdep.txt > log.txt &
#To specify options, please edit the the parameters below. Also, please keep the order of parameters.
#Parameter 1: The taxaRefBamMap file containing information of taxon and its corresponding bam files. The bam file should have .bai file in the same folder
#If one taxon has n bam files, please list them in n rows.
/Users/feilu/Documents/analysisL/softwareTest/pgl/popdep/inputfile/taxaBam.txt
#Parameter 2: The chromosome which will be scanned.
1
#Parameter 3: The length of the chromosome
1000000
#Parameter 4: The path of samtools
/usr/local/bin/samtools
#Parameter 5: Number of threads
16
#Parameter 6: The output file in gz format
/Users/feilu/Documents/analysisL/softwareTest/pgl/popdep/out/chr001_popdep.txt.gz
The parameter file is available from here.
One attached file is referenced in the parameter file. It is
- taxaBam.txt
This file contains taxa names, and bam files. The format is as follows.
Taxa "Bams(A list of bams of the taxon, seperated by the delimiter of Tab)"
TW0060 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0060.sub.bam
TW0061 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0061.sub.bam
TW0062 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0062.sub.bam
TW0063 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0063.sub.bam
TW0064 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0064.sub.bam
TW0065 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0065.sub.bam
TW0066 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0066.sub.bam
TW0067 /Users/feilu/Documents/analysisL/softwareTest/pgl/fastCall/bams/TW0067.sub.bam
The attached file is available from here.
The result is in the following format.
Position Depth_Mean Depth_SD
1 3.75 2.941742
2 3.85 2.9660473
3 4.65 3.4085112
4 5.0 3.559026
Author
Fei Lu
[email protected]; [email protected]
https://plantgeneticslab.github.io/home/
Citation
Coming soon.