Getting Started with Genome Mate Pro, Part 6 — The Chromosome Browser

If everything has gone to plan so far, you should have a sea of segments against a yellow background in the CHROMOSOMES tab.

Let’s explore some of the things you can do here and some of the settings that affect this tab.

 

The CHROMOSOMES Tab

  1. Open GMP and click on the CHROMOSOMES tab.
  2. Select Chr: 1 from the pull-down at the top left to look at chromosome 1. Now, select a different chromosome, say Chr: 7, and see how the segments change. Play around with this.
  3. Select Chr: X to look at the X chromosome. You should have some segments here, but there are more to be had. That’s because the GEDmatch Matching Segment Search only finds X segments for people who match you on other chromosomes as well. If you want the X segments for people who match you only on the X chromosome, we’ll have to import them another way. We’ll put it on our to-do list for now.
  4. If you’ve tested a parent, child, or full sibling, you may have noticed that their segments are missing. For example, neither my parents nor my kids are showing in the screenshot at the top of this post. Again, that’s because the GEDmatch Matching Segment Search skips close relatives to save processing time. Another to-do!
  5. Go back to Chr: 1 and let’s take the CHROMOSOMES tab for a spin. Notice that the green band across the top also has a search field, a set of check boxes, and a pull-down.  Right below that are a series of column headers against a white background.
    They are:
    • Profile — shows the short name for the profile that’s currently active (probably your profile right now)
    • Relative — name/alias of the person who matches on that segment
    • Side — lets you mark the segments as M (for maternal), P (for paternal), B (for both, e.g., a fully identical segment shared with a sibling), or I (for identical-by-chance); should just have question marks now because sides have not been assigned yet
    • Group — lets you cluster your DNA relatives into groups of your own naming; should be blank at the moment
    • Chr — the chromosome number; should be 1 now
    • Start and End points of each matching segment
    • cMs – the centimorgan “length” of each matching segment
    • SNPs — the SNP (single nucleotide polymorphism) count for each segment
    • Graphic — a visual map showing where the segment is along the chromosome’s length
  6. Assign a side to some of your matches. In my case, Nellie and Parrain are maternal relatives. For each of their segments, I can click the question mark in the “Side” column and enter the letter M (for maternal) in the blank. Shelley is paternal, so for her, I can enter P there.

    If you don’t know which of your DNA relatives belong to which side, just make up some assignments for now. Do some maternal (M), some paternal (P), and leave some as unknown (question mark).
  7. Click the column header called “Relative”. Click it again. Clicking here will sort the chromosome browser by relative name, toggling between A-to-Z or Z-to-A whenever you click it. Experiment with sorting by different columns to see what happens.
  8. Now, look at the check boxes in the green band above the column headers. These are filters. Uncheck the box beside “Maternal”.

    The segments you designated with Side = M should disappear.
  9. The “All Sources” pulldown on the far right lets you filter your chromosome browser by the database from which the segments originated.  Here, select “23andMe”.
    All of your segments should disappear, because we’ve only done a GedMatch import at this point. Don’t panic!  Simply select “GedMatch” or “All Sources” to make your segments reappear.  This pull-down is fabulous when you want to focus on segments from a single source.
  10. In the right half of that green band is the text “Hide Min:” then checkboxes for cMs, SNPs, and Length. These will let you hide segments based on criteria that are set in the Options: App Settings window (see Part 4). In my screenshot, I’ve hidden all segments shorter than 15 cM. Were I to uncheck the box, the short segments would appear in the chromosome browser. You can also set a maximum if you want to hide large segments and focus on medium or small ones.

Settings for the CHROMOSOMES Tab

In the OPTIONS: APP SETTINGS tab are some controls that will affect the CHROMOSOMES tab.

  1. Click on the OPTIONS tab, then APP SETTINGS at the top left.
  2. In the top-center panel are the settings for the CHROMOSOMES tab. Change the “Min cMs” to 30.

    Click the SAVE OPTIONS button at the bottom right. You’ll get a pop-up telling you that the settings have been saved.  Click OK to dismiss it.
  3. Switch back to the CHROMOSOMES tab. You should see far fewer segments, perhaps even none at all, because the setting hides segments smaller than the set value.
  4. Recall that in the CHROMOSOMES tab, we have a check box to toggle that threshold on or off.

    Uncheck the box, and your chromosome browser should fill with all of the imported segments for that chromosome, down to the threshold you set for the imports (probably 7 cM).
  5. Check the cMs box again, then switch back to the OPTIONS tab.
  6. In the OPTIONS tab, change the Min cMs back to 15 and then the “Number of days to highlight new matches” to zero.

    Click the SAVE OPTIONS button at the bottom right and acknowledge that the settings have been saved.
  7. Switch back to the CHROMOSOMES tab. Instead of the yellow highlighting, your segment information should now be displayed against a green and white striped background.  (Bonus points for anyone who recognizes the motif; you’re either old or very geeky … or both.)  Click on a match to highlight that segment in orange.

    The yellow highlighting is very useful when you are working with an established database, because it makes newly imported segments easy to find.  When all of the segments are newly imported, the yellow is not particularly helpful.
  8. Switch back to the OPTIONS tab and click the radio button to Display “Notes” instead of “Graph”.

    Click the SAVE OPTIONS button at the bottom right of the GMP window.
  9. Switch back to the CHROMOSOMES tab. Instead of seeing a segment map on the right-hand side, you’ll see comments indicating when the segment was added to GMP.  Once we add notes about the MRCA (in a future lesson), the “Added on” date will be replaced by the MRCA notes, as for Shelly in the screenshot.
  10. Go back to the OPTIONS tab and restore the settings to your preferred configuration. The screenshot shows the settings I use in my day-to-day work.  They’re easy to change, and you’ll eventually find ones that work for you.

 

 

In the next lesson, we’ll address the items on our to-do list. We’ll import the remaining segments for the X chromosome as well as segments for close relatives.

 

Getting Started with Genome Mate Pro Series

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