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Align Error - no bwa in path

Member
edited August 2012

I am trying to realign a .bam file to a new reference (ex: new.fasta), however when I run the task "Align", I am given the following error message:

no bwa in java.library.path

This same error message occurs with I try and use the task "AlignmentValidation". Do you know how I might fix this problem or another method to realign a bam file to a new reference?

Thank you.

• Charlestown, MAMember

Do you have BWA installed? Install it if you don't, and point the java library path to it, so the program can find it.

We recommend you use BWA on it's own if you're simply aligning a bam file. There is no need to use the GATK for that.

If you're going to reprocess the BAM file from scratch, take a look at our Best Practices and the Data Processing Pipeline script.

• I have the same problem with using cluster. Although I loaded both modules as following: