BAM Header minor edit

[seq_lover]

Hi,

I have around 20 BAM files and each of them have proper bam header including RG ID, Sample, Library, Platform unit, Description and Platform. I was reading the GATK manual and just realized that the only accepted names for platforms are 454, LS454, Illumina, Solid, ABI_Solid, and CG. But I wanted to be quiet specific when i was converting SAM to BAM and used "Solid5500XL" as the platform name.

I know there are AddorReplaceReadgroups and ReplaceSamHeader commands in Picard which i can use to edit the BAM header. But it will take some time as I have many large files. Is there an easy way to do so without rewriting the BAM files.

Thanks in advance.

[nilshomer]

No, you will need to rewrite the BAM files.

[seq_lover]

Thanks Nils.

[maubp]

You could use 'samtools reheader' which will avoid decompressing and recompressing all the read data, but does still have to copy it.

[seq_lover]

Thanks Peter,

It was way faster than I predicted.