How to change SM tag in bam file

Question

[ddzhangzz]

I have a bam file with header such like this:

@RG ID:S1-L001  LB:L001 PL:Illumina SM:L001 PU:novaSeq
@RG ID:S1-L002  LB:L002 PL:Illumina SM:L002 PU:novaSeq

This bam file was generated by picard MergeSamFiles where one sample library was sequenced in two lanes (L001, L002) but I need to correct the SM tag to a single library name such like:

@RG ID:S1-L001  LB:L001 PL:Illumina SM:S1   PU:novaSeq
@RG ID:S1-L002  LB:L002 PL:Illumina SM:S1   PU:novaSeq

What I tried

samtools view -H abc.bam > header.sam

and manually edit the SM tages in header.sam and reheader using samtools:

samtools reheader header.sam abc.bam

But the terminal printed out unrecogniziable characters and I thought something went wrong. Any suggestions?

Answer 1

[ATpoint]

reheader produces a new bam file with the altered header. In your command, it is send to stdout, and as bam is a compressed/non human-readable format, it looks weird on screen.

samtools reheader header.sam abc.bam > abc_reheadered.bam