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
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
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