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?
$ 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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