hi all
I'm changing part of the header in a number of bam files.
however, after I do that, the resulting bam file is truncated....
I used the following code:
samtools view -H file.bam | grep 'SN:X\|^@RG\|^@PG\|^@HD' | samtools
reheader - file.bam > bam_final/new_name.bam
and
samtools view -h bam_final/new_name.bam
gives me
[main_samview] truncated file.
right after the new header....
any idea how to fix this?
thanks
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