Pittsburgh Supercomputing Center 

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BWA

 

 

BWA comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Installed on blacklight, biou

Other resources that may be helpful include:

Li H. and Durbin R. (2009)
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60. [PMID: 19451168]
Li H. and Durbin R. (2010) 
Fast and accurate long-read alignment with Burrows-Wheeler Transform.
Bioinformatics, Epub. [PMID: 20080505]

Website: http://bio-bwa.sourceforge.net/

Running BWA

1) Make BWA availiable for use
a) blacklight:

The BWA program will be made availiable for use through the module command. To load the BWA module enter:

module load bwa

b) biou:
The BWA programs are availiable through the Galaxy instance on biou.

To make the BWA programs availiable through the command line, csh users should enter the following command:

% source /packages/bin/SETUP_BIO_SOFTWARE

To make the BWA programs availiable through the command line, bash users should enter the following command:

% source /packages/bin/SETUP_BIO_SOFTWARE

2) Usage:

a) First, index the fasta formatted reference sequence:

bwa index -a bwtsw ref.fa

b) Search reference with single (i.e. non paired-end) reads and create SAM file (using 16 threads):

bwa aln -t 16 ref.fa one.fq > single.sai
bwa samse -P ref.fa single.sai one.fq > aln-se.sam

c) Search reference with paired-end reads (using 16 threads):

bwa aln -t 16 ref.fa one.fq > pe_one.sai
bwa aln -t 16 ref.fa two.fq > pe_two.sai
bwa sampe -P ref.fa pe_one.sai pe_two.sai one.fq two.fq > aln-pe.sam

BWA Commands can be invoked as follows:

java jvm-args -jar BWACommand.jar OPTION1=value1 OPTION2=value2...

To see the command line arguments for an individual BWA command:

java jvm-args -jar BWACommand.jar --help

For example, to see the command line arguments for the BWA AddOrReplaceReadGroups command on blacklight enter:

java -XX:ParallelGCThreads=1 -jar $PICARD_TOOLS_HOME/AddOrReplaceReadGroups.jar

3) BWA Commands:

The following commands are availiable in the BWA package:

AddOrReplaceReadGroups
BamToBfq
BamIndexStats
BuildBamIndex
CalculateHsMetrics
CleanSam
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectInsertSizeMetrics
CollectMultipleMetrics
CollectTargetedPcrMetrics
CollectRnaSeqMetrics
CompareSAMs
CreateSequenceDictionary
DownsampleSam
ExtractIlluminaBarcodes
EstimateLibraryComplexity
FastqToSam
FilterSamReads
FixMateInformation
IlluminaBasecallsToFastq
IlluminaBasecallsToSam
CheckIlluminaDirectory
IntervalListTools
MakeSitesOnlyVcf MarkDuplicates
MeanQualityByCycle
MergeBamAlignment
MergeSamFiles
MergeVcfs
NormalizeFasta
ExtractSequences
QualityScoreDistribution
ReorderSam
ReplaceSamHeader
RevertSam
SamFormatConverter
SamToFastq
SortSam
VcfFormatConverter
MarkIlluminaAdapters
SplitVcfs
ValidateSamFile
ViewSam
Building

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