Using samtools to analyze bwa output

niteesh.prasad · 03-10-2012, 09:24 PM

I have a query file with 70,000 lines of sequences and when I do the

Code:

bwasw

each sam output file is about 35 mb and obviously contains all the sequence lines. I need to perform the alignment on about 1000 files, so you can imagine that I don't want to have 35 gigs worth of output to sort.

I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail.

Code:

./samtools view -bS -f 4 testing.sam > output.bam

All my sam files give the following error:

Code:

[samopen] SAM header is present: 1 sequences.
[sam_read1] reference '0' is recognized as '*'.
Parse warning at line 3: mapped sequence without CIGAR
Parse error at line 3: missing colon in auxiliary data
Aborted (core dumped)

Here's what a part of my sam files looks like

Code:

@SQ	SN:gi|89106884|ref|AC_000091.1|	LN:4646332

	4	*	0	0	*	*	0	0	<CGTAAAAAGGA> 	*
	4	*	0	0	*	*	0	0	<TAGCCGTAGGG>   *

I'd appreciate help with this!

nilshomer · 03-11-2012, 08:40 AM

There's no read name in the SAM records you list.

niteesh.prasad · 03-11-2012, 09:10 AM

But this is the output I get from bwa. how should i fix this?

nilshomer · 03-11-2012, 09:21 AM

Post the BWA help mailing list. It looks like a bug to me. Make sure you include a test case.

niteesh.prasad · 03-11-2012, 09:26 AM

Before I do that, I want to make sure I am not wrong. Here is the code I used for the bwa:

Code:

./bwa bwasw INDEXES/AC_000091.fna QUERY/635plus104_500bp_reads.fasta > results.sam

The input AC_000091.fna was the indexes created with the following command:

Code:

./bwa index AC_000091.fna "AC_000091.fna";

and the query file was a FASTA sequence file.

So, in theory this should have worked?

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03-10-2012, 09:24 PM	#1
niteesh.prasad Junior Member Location: PA Join Date: Feb 2012 Posts: 6	Using samtools to analyze bwa output I have a query file with 70,000 lines of sequences and when I do the Code: bwasw each sam output file is about 35 mb and obviously contains all the sequence lines. I need to perform the alignment on about 1000 files, so you can imagine that I don't want to have 35 gigs worth of output to sort. I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail. Code: ./samtools view -bS -f 4 testing.sam > output.bam All my sam files give the following error: Code: [samopen] SAM header is present: 1 sequences. [sam_read1] reference '0' is recognized as ''. Parse warning at line 3: mapped sequence without CIGAR Parse error at line 3: missing colon in auxiliary data Aborted (core dumped) Here's what a part of my sam files looks like Code: @SQ SN:gi\|89106884\|ref\|AC_000091.1\| LN:4646332 4 0 0 * * 0 0 <CGTAAAAAGGA> * 4 * 0 0 * * 0 0 <TAGCCGTAGGG> * I'd appreciate help with this!

03-11-2012, 09:26 AM	#5
niteesh.prasad Junior Member Location: PA Join Date: Feb 2012 Posts: 6	Before I do that, I want to make sure I am not wrong. Here is the code I used for the bwa: Code: ./bwa bwasw INDEXES/AC_000091.fna QUERY/635plus104_500bp_reads.fasta > results.sam The input AC_000091.fna was the indexes created with the following command: Code: ./bwa index AC_000091.fna "AC_000091.fna"; and the query file was a FASTA sequence file. So, in theory this should have worked?

03-11-2012, 08:40 AM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	There's no read name in the SAM records you list.

03-11-2012, 09:10 AM	#3
niteesh.prasad Junior Member Location: PA Join Date: Feb 2012 Posts: 6	But this is the output I get from bwa. how should i fix this?

03-11-2012, 09:21 AM	#4
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Post the BWA help mailing list. It looks like a bug to me. Make sure you include a test case.