Hi Yifeng,
Can you post one of the headers (preferably the one from the first file
that you specified in the merge command)? Am I correct in assuming that you
didn't use the "-h inh.sam" option?
In general, this error means that there's something about the header file
that samtools is trying to write to the merged file that it can't quite
parse correctly.
Best,
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<devon.r...@dzne.de>
On Fri, Nov 28, 2014 at 2:43 AM, <yif...@cmmt.ubc.ca> wrote:
> Hi,
>
> I can successfully merge two bam files (replicates from ENCODE) using
> samtools version 0.1.19, but got an invalid header error with version 1.1.
> Is there anything I need to do with the parameters of v1.1, in order to be
> consistent with v0.1.19?
>
> Thanks,
>
> Yifeng
>
>
>
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