SAM file without a header. Can't convert to BAM

[Malfet]

Hi, guys! I'm a complete noobie in computational staff and just trying to learn thing. I want to convert SAM file to BAM and my SAM file does not have a header.
So, I goggle the problem and found one possible solution with -t options from samtools. I created the reference.fa.fai with

samtools faidx reference.fa

command and then tried to run

samtools view -Sb sam.file -t reference.fa.fai  >  bam.file

However, I'm getting the error message

[sam_header_read2] 35 sequences loaded.
Parse error at line 2: missing colon in auxiliary data
/var/spool/sge//node091/job_scripts/1441097: line 10: 19514 Aborted                 (core dumped) samtools view -Sb $in_file.sam -t /$

I've tried to use advices from here http://seqanswers.com/forums/showthread.php?t=9650, but still keep getting the same error message.

Please, help!

[FractalExpression]

Maybe try ReplaceSamHeader in Picard http://picard.sourceforge.net/comman...placeSamHeader

[Richard Finney]

Try googling/duckducking your error message ...
"missing colon in auxiliary data"

See previous discussions:

http://seqanswers.com/forums/showthread.php?t=9650

http://seqanswers.com/forums/showthread.php?t=14902

Sounds like "aux" means the stuff after QUAL(quality filed) in a SAM line (i.e. a text version of the bam record).
(See line 367 of samtools-0.1.18/bam_import.c ). There's probably invalid OPT (aux) data. That is, the additional annotation information is not properly formatted. Some extra data got a colonectomy or something. (sorry). Just cut out all of the the OPT (aux) data if you don't need it ... something like this ...

cat original.sam | cut -f1-12 > new.tmp.sam

or somesuch.

[dpryan]

As Richard mentioned, this means that one of the "tags" in the auxiliary section (the stuff following the quality scores) is malformed. This error is thrown if a tag, including the colons, is less than 6 characters long, or is lacking a colon as the third or fifth character. You might get lucky and just be able to fix the second line of your SAM file in a text editor. Otherwise, you'll need to either cut out the auxiliary info or do a search and replace on the whole file, replacing the affected tag(s).

[Malfet]

Maybe try ReplaceSamHeader in Picard http://picard.sourceforge.net/comman...placeSamHeader

Thank you very much! Looks like it worked... the resulting file is slightly smaller, that's strange, but end of my old file without header and end of this file are identical, so I'll try to proceed with it further and see what will happen.

Thanks for your help.

[Malfet]

See previous discussions:

http://seqanswers.com/forums/showthread.php?t=9650

http://seqanswers.com/forums/showthread.php?t=14902

I tried to follow these advices, but it did not help me and I was still getting the same error message. However, it looks like that the Picardtools suggested by FractalExpression worked, so I'll try to proceed the file.

[swbarnes2]

Try

samtools view -Sbh sam.file   >  bam.file

instead