Samtools 'import' and lost read group header

[mrxcm3]

I am pretty new to manipulating NextGenSeq datasets, so my apologies if this question is trivial!

I want to format my .bam files so I can use them in GATK for SNP calling. Although my .bam files have all the necessary 'read group' information, they are sorted in an lexicographical order - which will not work with GATK.

However, if I resort my .bam so the headers are replaced by the reference using;

samtools import <your reference>.fai <your file>.sam <your file>.sorted_header.bam

then my read group header disappears - and GATK wont work! Most annoying! Does anyone know of a way to either avoid this when resorting, or adding the '@RG' header afterwards?? Thanks

[maubp]

Try "samtools reheader" to replace the BAM header.

[mrxcm3]

Thanks maubp this has worked