colored mutations

[Joerg]

Hello,

Could you elaborate a bit more on how to color different mutations, please?

I've just loaded a fasta genome and a mutation .mut file and I see all mutations in black, although they apparently are in a "distinct track" since I have nothing to link to yet. The values in the 'type' column of the .mut file are labeled according to the existing mutation classes on the color legend window (Missense, Synonymous, ...). What do I do wrong?

Can I also add more mutation classes, i.e. does IGV reads/accepts all possible 'type' values from .mut files and offers the user to specify a color for each of them?

Here is a digest of my mut file:
chr    start   end     sample  type    BPchange    gene    AAchange     codon
chr07  9851    9851    Pools_and_Parents   Other likely neutral    G->A
chr07  10073   10073   Pools_and_Parents   Other likely neutral    T->C
chr07  10990   10990   Pools_and_Parents   Synonymous    G->A    BGIOSGA024990   C->C    TGT
chr07  11022   11022   Pools_and_Parents   Missense      G->T    BGIOSGA024990   H->N    AAC

Any help is greatly appreciated.
best, Jörg

[Jim Robinson]

Hi Jörg,

You need to select "Color code mutations" int the Preferences windows  (View > Preferences > Mutations).  You can add your own classes, and colors will be arbitrarily chosen for them.  Currently you can't edit these colors.   This is a known problem,  we are working on a color editor for arbitrary mutation labels, it will be available soon.  

Apologies for the delayed response, 

Jim

[Joerg]

Dear Jim,

thank you for your answer.
In your last email you indicated that new classes will be assigned arbitrary additional colors. However, I find that whatever I write into the mutation type column all are displayed in the same color ("other", pink). I do have a few additional types to annotate, e.g., newly produced START codons, intronic, intergenic, etc. It would be nice if you could point me towards my mistake.

Furthermore, when trying to display all the pre-defined mutation types using following mock .MUT file:

chr07    20129204    20129204    .    Indel
chr07    20129205    20129205    .    Nonsense
chr07    20129206    20129206    .    Targeted Region
chr07    20129207    20129207    .    Target    Region
chr07    20129208    20129208    .    Other
chr07    20129209    20129209    .    Synonymous
chr07    20129210    20129210    .    Truncating
chr07    20129211    20129211    .    Splice site
chr07    20129212    20129212    .    Missense
chr07    20129213    20129213    .    Other AA changing
chr07    20129214    20129214    .    Unknown
chr07    20129215    20129215    .    Non-coding Transcript
chr07    20129216    20129216    .    Indel

it seems as if "Indel", "Nonsense", "Synonymous", "Truncating", "Missense" and "Unknown" yield a distinct color, whereas all others are subsumed under one color (pink). I noticed that they happen to be the ones without a space in the name. I tried to trick this by escaping the white space as well as by quoting, however, with no luck.

Thanks for any explanation!

best,
Jörg

[Jim Robinson]

Hi Jörg,

This problem has been resolved and the fix committed to the "early access" IGV.   It will be included in the next bug-fix release, version 2.1.21,  sometime in the next week.   In the meantime you can access the early access version from the link on the downloads page.

-- Jim