BWA mem

[Venice Margarette Juanillas]

Hi,

I was trying to use BWA-MEM in aligning the tags to the reference genome. I'm successful in generating the sam output but it upon trying to convert SAM to TOPM, I've been getting this error:

...

...

Found 187158 tags in SAM file.  Assuming BWA file format.

Catch in reading SAM alignment file at tag 0:

        length=64count=11       0       2       22880099        60      64M    *          0       0       CAGCAAAAAAACATCCAATCCAACCTACGCGCGCAAGACCAAAAGGAAGCCGTCCGCCGCCGGC          ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff        NM:i:0 AS:i:64  XS:i:0

Error: java.lang.NullPointerException

java.lang.NullPointerException

        at net.maizegenetics.gbs.maps.TagsOnPhysicalMap.parseSAMAlignment(TagsOnPhysicalMap.java:673)

        at net.maizegenetics.gbs.maps.TagsOnPhysicalMap.readSAMFile(TagsOnPhysicalMap.java:615)

        at net.maizegenetics.gbs.maps.SAMConverterPlugin.performFunction(SAMConverterPlugin.java:55)

        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)

        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

What should I do?

Thanks and Best Regards,

Venice

[Jeff Glaubitz]

Hi Venice,

 

BWA aln produces an “XO” field (=number of best hits) while BWA mem doesn’t (causing the null pointer exception).  So far, the SAMConverterPlugin only works with

(1) BWA aln, or

(2) bowtie2 with the default, one output line per query, option.

 

For now, please use either BWA aln or bowtie2.

 

Best,

 

Jeff

 

--

Jeff Glaubitz

Project Manager

Biology of Rare Alleles in Maize and its Wild Relatives

National Science Foundation award IOS-1238014

http://www.panzea.org

Institute for Genomic Diversity

Cornell University

175 Biotechnology Bldg

Ithaca, NY 14853

Phone: 607-255-1386

jcg...@cornell.edu

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[Venice Margarette Juanillas]

Hi Jeff,

Thanks for the reply. I'll stick to BWA aln then.

Best Regards,

Venice