SampleValidation

Welcome to the SiPAS-tools wiki!

Overview

SampleValidation app aims to identify RNA samples name. It uses IBS distance to find the most probable name.

Prerequisites

Java 8
http://www.oracle.com/technetwork/java/javase/overview/java8-2100321.html

Samtools
http://samtools.sourceforge.net/

Usage

From command line,

• java -Xmx100g -jar SiPAS-tools.jar -a SampleValidation -f ./SampleValidation_parameter.txt > log.txt &

The content of the parameter file is as follows.

@Author: Xiaohan
@Email: xhanyang@genetics.ac.cn

#This hapscanner pipeline is used to test the IBS matrix and give the final possible samples

#####File parameter -- genotypeDir,bamDir,outputDir,plate
#Parameter1:	GenotypeDir
/data1/home/junxu/genotypeMaf005

#Parameter2:	BamDir
/data2/junxu/SiPAS-tools/1_0

#Parameter3:	plate
1_0

#Parameter4:	OutputDir
/data2/xiaohan/hapscanner/outputNew

#######Hapscanner parameter -- parameterDir,taxaRefBAMDir,posDir,posAlleleDir,referenceDir
#Parameter5:	parameterDir
/data2/xiaohan/hapscanner/parameter

#Parameter6:	taxaRefBAMDir
/data2/xiaohan/hapscanner/taxaRefBAM

#Parameter7:	posDir
/data2/xiaohan/hapscanner/poseQTL

#Parameter8:	posAlleleDir
/data2/xiaohan/hapscanner/posAlleleeQTL

#Parameter9:	referenceDir
/data2/xiaohan/hapscanner/ref

######utils
#Parameter10:	samtools
/data1/home/xiaohan/miniconda3/bin/samtools

#Parameter11:	thread
12

#Parameter12:	chrNumber
42

########SampleValidation parameter -- 
#Parameter13:   rate
0.4

#Parameter14:   Qcdir
/data2/xiaohan/fastqc/1_0

#Parameter15:   QCmethod
median

The file is available here.

Author

Xiaohan Yang
https://github.com/Yangxiaohan0120

Song Xu
https://github.com/XscapeCn

Jun Xu
https://github.com/Junjun-Xu

Fei Lu
flu@genetics.ac.cn; dr.lufei@gmail.com
https://github.com/Fei-Lu