What does the @HD GO record type mean in a BAM file?

When I ran samtools to check if my bam file is right, it shows as this,

[rzeng@qlogin2 reference]$ samtools view -H MO_137.bam

@HD    VN:1.4    SO:coordinate
@SQ    SN:chr10    LN:130694993
@SQ    SN:chr11    LN:122082543
@SQ    SN:chr12    LN:120129022

My previous bam file looks like this,

$ samtools view -H /path/to/my.bam
@HD     VN:1.0  GO:none SO:coordinate
@SQ     SN:1    LN:247249719
@SQ     SN:2    LN:242951149

My question is what is GO:none mean? Why it shows in my previous bam file but not this file? I use the same pipeline with no any modification.

bam

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updated 4.5 years ago by Ram

• written 11.8 years ago by zengtony743

1 answer

Looking back at historical SAM spec documents it appears that the @HD GO: tag was removed in the transition from v1.2 to v1.3 of the file format. Obviously your earlier file (VN:1.0) predates this change and your recent one (VN:1.4) comes after.

The GO tag stood for "Group Order" and apparently had something to do with group-wise sorting of the SAM file. Here is the info from the SAM Spec v1.2 document:

GO Group order (full sorting is not imposed in a group). Valid values are: none, query or reference

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updated 4.5 years ago by Ram

• written 11.8 years ago by kmcarr00

Thank you for your explanation!

I have another previous bam.file like this. it was VN:1.4 but it also has GO:none. I checked my previous samtools version (0.1.19) and current samtools that I am using having version as (1.1). So is that because version (1.1) has removed GO: none but not in version 0.1.19? Anyway.. My new Bam file looks fine.

[rzeng@prism reference]$ samtools view -H H.bam

@HD    VN:1.4    GO:none    SO:coordinate
@SQ    SN:chr10    LN:130694993
@SQ    SN:chr11    LN:122082543
@SQ    SN:chr12    LN:120129022
@SQ    SN:chr13    LN:120421639

• 0 views • link

updated 4.5 years ago by Ram

• written 11.8 years ago by zengtony743