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Old 07-11-2011, 12:08 PM   #1
Hkins552
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Location: Baltimore MD

Join Date: Jun 2011
Posts: 18
Post samtools view error after reheader

I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs I think attempted the conversion and received the following output:

$ samtools view -bS 1112-1.reheader.sam > 1112-1.reheader.bam

[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
[sam_read1] reference 'chr1' is recognized as '*'.
etc.

Basically for an endless number of lines.

Has anyone seen a similar error?
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