Soap2Sam.Pl No Headers In Sam File
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 ?
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Ram
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Saket Choudhary
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Saket Choudhary
1 answer
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.
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Ram
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Philipp Bayer
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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...
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Ram
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Philipp Bayer
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Philipp Bayer
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