My Reconstruction Workflow

This post documents the process I have followed and the various steps involved in attempting to reconstruct Abigail Courtney’s genome, as part of my research to identify her father, George.

Not all tools used align neatly with one another, which meant there was unavoidable duplication of data entry during analysis. I trialled several ways of recording and managing the information, including within my DNA database (GDAT) and through multiple chromosome maps at DNA Painter (DNAP).  Each approach offered distinct advantages, but none provided a complete or perfect solution on its own.  I've documented the process for historical purposes and hope that the steps may be of use to others undertaking an endeavour such as this.  

For a more conceptual overview of the approach, see my earlier outline from 2021: Recreating the Genome of Abigail Courtney.



What follows reflects my working process as at December 2025: 

Step Task Where Outcome Note
1 Identify all DNA testers that will contribute to identifying George Courtney, my M2GGF Manual 14 descendants tested. This includes 4 great grand children, 8 great great grandchildren and 2 great great great grandchildren Whilst children don’t contribute additional DNA, their kits are useful for validating IBD and assigning sides
2 Use the DNA Coverage Estimator to identify how much DNA we potentially can identify from the George Courtney descendants DNAP 30.1% of his DNA, with no potential for more living testers Is 30.1% enough DNA to identify him?
3 Create Phased (M/P1) and Evil Twin (M/P2) kits for any parent/child combination in the DNA testers GEDmatch 3 sets of parent/child DNA testers (Roberts-Murphy side only) Work with these (M/P1 and M/P2) kits as much as possible, rather than the original kit to eliminate false matches
4 Undertake Visual Phasing for the 4 Roberts-Murphy siblings (RMS - great grandchildren) to identify segments inherited from their 4 grandparents including PGM Abigail Courtney Manual using GEDmatch data Identify the segments inherited by the daughter of George Courtney - Abigail Courtney (PGM of RMS) Coverage estimator suggests we have approx 60.2% of Abigails DNA (from all descendants not just RMS)
5 Compare the DNA matches for all Phased and Evil Twin kits to ensure they align with the grandparent lines in RMS_VP output. If not, review VP. Manual using GEDmatch data When VP and phased kits align they validate the assumptions made in the VP process Phased kits will help identify the crossover points more accurately. Phased kits only have one side.
6 Undertake Visual Phasing for the 4 Roberts-Reidy siblings (RRS - great great grandchildren) to identify segments inherited from their PGF James George Roberts (JGR) Manual using GEDmatch data Identify the segments inherited by James George Roberts, son of Abigail Courtney (paternal uncle of RMS) Coverage estimator suggests we have approx 46.8% of James’ DNA (From his RRS grandchildren) and 98.75% of his son BLR (father of RRS)
7 Create a spreadsheet to consolidate the segment data output, tabs by chromosome, then list by segment locations for each mapped ancestor (colour code to align with VP data). Have a column for all kits, including phased and Evil Twin outputs. Manual using VP output Visual representation of likely ancestor groups by segment location for each chromosome. Enables easy reference point to assess new matches, see which kits should match before allocating to likely ancestor group
8 Create a column to summarise the segments inherited by EAR (father of RMS) and JGR (PGF of RRS) by chromosome and segment locations (Roberts-Courtney segments) Manual using spreadsheet Consolidated segment data by chromosome for EAR and JGR (the two sons of Abigail Courtney) * EAR data will have 2 sides (RMS_VP identified PGF Roberts and PGM Courtney).    * JGR data will only have 1 side (RRS_VP only identified their PGF - JGR brother of EAR - mix of Roberts-Courtney)
9 Double check the DNA matches for all Phased and Evil Twin kits to ensure they align with the grandparent lines in RMS and RRS_VP output. If not, review VP. Manual using GEDmatch data When VP and phased kits align they validate the assumptions made in the VP process Phased kits will help identify the crossover points more accurately. Phased kits only have one side.
10 Create Lazarus kits for both fathers (parental side of interest) for the 2 sets of VP siblings (EAR and BLR) then run segment search for each kit GEDmatch and spreadsheet Matches to descendant kits in segment search report should align with allocated ancestor segments Segment Search data can be input to GDAT, DNAP or both, for ongoing segment analysis of other non descendant matches
11 Create a chromosome map at DNAP using the data in the RC column for BLR - Father of RRS siblings. Start with uploading a ‘GEDmatch one on one’ with the EAR Lazarus kit, mark them 'Shared with RMS'. Manually add remaining segments for 'RRS only' and other confirmed cousins not on GEDmatch.  DNAP, spreadsheet and GEDmatch Chromosome map containing 1 side - mix of Roberts and Courtney. What BLR inherited - from RRS_VP and inferred mapping Preparation for uploading to Borland Genetics. Use different colour codes for ‘Shared with RMS’,  ‘RRS only’ and 'Other Confirmed Matches' (eg 23&Me, MyHeritage, FTDNA and LivingDNA
12 Create a chromosome map at DNAP using the data in the RC column for EAR - Father of RMS siblings DNAP and spreadsheet Chromosome map containing 2 sides - Roberts and Courtney. What EAR inherited - from RMS_VP and inferred mapping Preparation for uploading to Borland Genetics
13 Use DNAP map to create profiles at Borland Genetics for EAR and BLJ DNAP and Borland Profiles for matching within Borland Input to reconstruction of Abigail Courtney profile at Borland (daughter of George)
14 Continue to identify MRCA’s for Courtney/Paice segments Segment Analysis Split Abigail segments into paternal (George) and maternal (Paice) sides Aim to reconstruct enough DNA for Abigail to build a Lazarus kit at GEDmatch (>1500cMs =  approx 21%)


                                                                      **********

This blog is dedicated to finding my second great grandfather Arthur 'George' Courtney c1841. To see a summary of my research click here. 

If you can help answer any questions raised in this blog, please contact me via the contact form on the sidebar on this page, or send me a private message via Wikitree, Ancestry or Facebook. 

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