1. Major third party Software

    bwa-0.6.1-r104
    picard-tools-1.69
    samtools-0.1.16
    GATK
    SeqWare

2. Preparing reference database

3. Alignment against reference database

	
Script dir: /ddn/gs1/home/li11/project2012/blackShearProject/scripts
 
	
SeqWare script: /ddn/gs1/home/li11/svnroot/seqware/trunk/seqware-pipeline/perl/bin/sw_module_BWA.pl

	
Command: perl batchAln.pl –inDir /ddn/gs1/project/nextgen/post/black009/NG-14-Stumpo-Blackshear/ –outDir /ddn/gs1/home/li11/project2012/blackShearProject/resultsDir/

4. Getting alignment QC assessment

	
alignStat
perl batchAlignStat.pl –inDir /ddn/gs1/home/li11/project2012/blackShearProject/resultsDir/ –outDir /ddn/gs1/home/li11/project2012/blackShearProjec/alignStatDir/


Remove duplicate: bash rmdup.sh 19U_R1 ~/project2012/BEexome/BWA_hg19/19U_GCCAAT_L005_R1_001_bwa_gnm.bam ~/project2012/BEexome/BWA_hg19/19U_GCCAAT_L005_R1_SE_rmdup.bam ~/project2012/BEexome/BWA_hg19/ >  19U_R1_SE_rmdup.log

AlignMetric: results will be generated from "remove duplicate script"

Coverage (need captured regions)


					

Okay, this question turns out more complex that I thought and it deserves a separate page.

People used SNVMix in the past, from the Original paper and anotherNature paper. However, it seems out of date as they are still focusing on old aligner — MAQ and old pileup format output from samtools

Another post on biostar indicates that both samtools and GATK will do the work.

Okay, let’s take a look at JointSNVMix

Samtools

• Download the source: wget http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2/download
• Upzip the tar ball: tar -xvjpf
• Build executable: Make