Sort/Color by tag not working for tags other than ID or SM under @RG header record

[Obi Griffith]

In the IGV documentation it is stated that it is possible to sort/color by TAG: "Tag allows custom input of a two-letter tag as designated in the SAM format file header section". This works for some tags (e.g., RG, SM) that are already available as separate options (read group, sample) and other tags that are summarized in read details (e.g., NM, MQ, etc). But it does not allow sorting/coloring by, for example, LB (library). I have bam files with read group tags as follows:

@RG ID:2896008004 LB:H_OX-08-0075-129-1325285-lg2-lib1 PL:ILLUMINA PU:HNTHTCCXX.5 SM:H_OX-08-0075-129-1325285

It would be a very useful feature if I could color by library (LB) to see how many independent libraries in a pooled sample support a variant, for example. Is it possible to do/add this?

[Jim Robinson]

Library is not a sam record tag, it is an attribute of the read group header.   Each sam record may have an RG tag, if present this tag refers to the ID field of the @RG header.  

I agree this would be a useful feature,  It would require a new synatx,  and probably only work for @RG properties since a special relationship is defined between the RG sam record tag and the @RG:ID property in the header.   Again this isn't really coloring by tag, but I get what you are trying to do.

If you are able please file a git issue at github.com/igvteam/igv/issues.  Regardless I will note this request.

Jim

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[Jim Robinson]

I've added an explicty "color by library" option.  This is available now in the snapshot version at http://software.broadinstitute.org/software/igv/download_snapshot.   It will be included in the next release.