samtools sam file no headers

[Irina Pulyakhina]

Dear all,

I have the following problem: my sam file contain no headers, so I can't convert it to bam directly, I get the following error:

> samtools view -S accepted_hits.sam
The tag [ID] required for [PG] not present.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

With previous version of samtools you could use "-t" option for this case, but now it doesn't exist anymore:

> samtools view -tS accepted_hits.sam
The tag [ID] required for [PG] not present.
[main_samview] fail to open "accepted_hits.sam" for reading.

So does anyone now how to create bam file from a sam file without headers?

Thanks in advance,
Irina

[cjp]

You can try -T ref.fasta (or -t):

samtools view -T /path/to/ref/fasta accepted_hits.sam

Chris