[Samtools-help] truncated file after reheader

[Seb <seb...@gm...>]

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