bwa0.5.5 doesn't output SAM header??

[krobison]

I just aligned some sequences with bwa0.5.5 (running under ubuntu) and when I tried to run samtools on the file it balked -- and on inspection the file lacks the sequence headers (@ lines)

Am I mistaken that the program used to include these? Is there a command line flag to trigger inclusion?

thanks

[KevinLam]

Why not use the latest version of BWA?

anyway perhaps if you post your command and maybe what the file is SAM? BAM? I can have a better idea

[krobison]

I'm looking at the sourceforge page http://sourceforge.net/projects/maq/files/ and BWA 0.5.0 appears to be the most recent version; am I looking at the wrong sourceforge page?

Here is the complete shell script

bwa aln -t 6 hg18.fasta SRR018003_1.fastq >  SRR018003_1.fastq.sai
bwa aln -t 6 hg18.fasta SRR018003_2.fastq >  SRR018003_2.fastq.sai
bwa sampe hg18.fasta  SRR018003_1.fastq.sai  SRR018003_2.fastq.sai SRR018003_1.fastq  SRR018003_2.fastq > SRR018003_1.pe.sam
samtools view -uS SRR018003_1.pe.sam |samtools sort - SRR018003.pe.sorted

samtools complains in that last line that the input file lacks a header

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

[jmarshall]

It's moved to its own project at http://bio-bwa.sourceforge.net/ -- perhaps Heng could make this more explicit on the maq pages.

BWA has generated @SQ headers since 0.5.2.

[Richard Finney]

Break last line into two commands:

${SAM} view -b -S x.sam > x.bam
${SAM} sort -n -m 17179869184 x.bam x.sort