Versions Compared

Old Version 4

changes.mady.by.user Deatherage, Daniel E

Saved on

compared with

New Version Current

changes.mady.by.user Deatherage, Daniel E

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

No Format
titleexample output of sample solution
collapsetrue
     1234 0/01	0/1	0/0
      520 0/01	0/10	0/1
      320 0/10	0/01	0/0
      414 0/1	01/01	0/10
      86 0/10	0/1	0	1/1
      434 01/1	01/1	0/0
      241 01/1	10/1	0/0
      1 10/1	0/1	0
0	0/0
Expand
titleDiscussion of the output

Overall this data is consistent with column 1 (NA12878) being the child. Lines marked with an * are inconsistant:

     34 0/1	0/1	0/0

     20 0/1	0/0	0/1

     20 0/0	0/1	0/0

     14 0/1	1/1	0/0	# middle can't be child
      6 0/0	0/1	0/1

      4 1/1	1/1	0/0	* No mendelian combination exists
   1 1/1	0/1	0/0

      1 0/1	0/0	0/0
Expand
titleDiscussion of the output

Here is my interpretation of the data:

1) This method effectively looks at a very narrow genomic region, probably within a homologous recombination block.

2) The most telling data: the child will have heterozygous SNPs from two homozygous parents.

3) So all this data is consistent with column 1 (NA12878) being the child:

	 12 0/0	0/1	0/0
      5 0/0	0/1	0/1
      4 0/1	0/0	0/1
      8 0/1	0/0	1/1
     43 0  1 1/1	0/1	0/0
	*
     24 0/1	1/1	0/0

"Outlier" data are:

      3 0/1	0/0	0/0      1 1/1	0/1	0/0*
 

This is, in fact, the correct assessment - NA12878 is the child.

...