<p>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.</p>

<p>Is there a way I can add headers to the SAM file ?</p>

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.