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Old 06-30-2010, 11:24 PM   #1
Location: honston

Join Date: Nov 2009
Posts: 27
Default BWA - samtools problem

Hello everyone

There are some topics concerning BWA and Samtools, but i still can't find the reasons of the trouble.

Here is what I count

bwa index -a bwtsw human.fasta
bwa aln human.fasta read.fq > aln_sa.sai
bwa samse human.fasta aln_sa.sai read.fq > aln.sam
samtools view -b -h -S -T human.fasta aln.sam > aln.bam
samtools sort aln.bam aln.sort
samtools index aln.sort.bam

when i finished these steps and get the sorted bam file, i then run

java -jar ViewSam.jar I=aln.sort.bam

it got the following error message:

Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 1, Read name 1_R9DycrMpuN1, MRNM should not be set for unpaired read.
at net.sf.samtools.SAMUtils.processValidationErrors(
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(
at net.sf.samtools.BAMFileReader$BAMFileIterator.<init>(
at net.sf.samtools.BAMFileReader.getIterator(
at net.sf.samtools.SAMFileReader.iterator(
at net.sf.samtools.SAMFileReader.iterator(
at net.sf.picard.sam.ViewSam.doWork(
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(
at net.sf.picard.sam.ViewSam.main(

how can i fix this?
genelab is offline   Reply With Quote
Old 07-02-2010, 05:53 AM   #2
Senior Member
Location: Boston

Join Date: Feb 2008
Posts: 693

Give the first line of your alignment, by samtools.
lh3 is offline   Reply With Quote
Old 07-02-2010, 11:13 PM   #3
Location: honston

Join Date: Nov 2009
Posts: 27

I have found one way to figure out the problem

I used the function "setValidationStringency" in samtools

genelab is offline   Reply With Quote

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