Soap2Sam.Pl No Headers In Sam File

Question

[Saket Choudhary]

When I convert a SOAP Paired end output to a SAM file using the soap2sam.pl script(http://soap.genomics.org.cn/down/soap2sam.tar.gz) my SAM file headers turn out to be empyty.

Is there a way I can add headers to the SAM file ?

Answer 1

[Philipp Bayer]

You can add the headers using samtools view:

samtools view -bT your_reference.fasta your_input.sam > your_input.bam

Use samtools view -H your_input.bam to check whether the header was added.

[Quak]

How about if you don't have the reference?

[Philipp Bayer]

See older question here: Is It Possible To Generate A Sam Header Without Any External Header Information?

I guess technically, it's possible - you would have to parse out all present chromosomes from your SAM file, and the 'last' alignment that appears for each, and use that as the length.. But I don't think there's any script for that...