How to add the CreateSequenceDictionary.jar to the sam file which doesnt have a Sequence Dictionary?
Hi, I have a sam file which was aligned using bwa aln and sampe command under default parameters due to which the sam file lacks a Header therefore I can not sort the sam file.
Kindly Help
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Pierre Lindenbaum
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yoh1242 •
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yoh1242 •
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the sam file lacks a Header
bwa always add a header:There must be something wrong with your command.
Furthermore CreateSequenceDictionary doesn't exist anymore, it's now included in a picard.jar .
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Pierre Lindenbaum
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How do you know it lacks the header and what is the full command you used for alignment and maybe postprocessing?