{"id":1861,"date":"2016-10-20T17:11:01","date_gmt":"2016-10-20T17:11:01","guid":{"rendered":"http:\/\/www.jmhartley.com\/HBlog\/?p=1861"},"modified":"2017-04-13T11:37:09","modified_gmt":"2017-04-13T11:37:09","slug":"raw-dna-phasing-of-4-siblings-using-one-parents-dna-part-6","status":"publish","type":"post","link":"http:\/\/www.jmhartley.com\/HBlog\/2016\/10\/20\/raw-dna-phasing-of-4-siblings-using-one-parents-dna-part-6\/","title":{"rendered":"Raw DNA Phasing of 4 Siblings Using One Parent’s DNA: Part 6"},"content":{"rendered":"

In my last Blog<\/a>, I was still playing catchup in going from my original 3 sibling phasing, to incorporating my brother’s new DNA results.<\/p>\n

Missing Principle 2 for Jon<\/h4>\n

Here is Principle 2 from the Whit Athey Phasing Paper I’ve been using:<\/p>\n

Principle 2 –If data from one of the parents are available, and that parent is homozygous at a SNP location, then another almost trivial phasing is possible<\/em><\/div>\n
since obviously that parent had to send the only type of base s\/he had at that location to the child<\/em><\/div>\n
<\/div>\n
I checked this in MS Access. Here is the query:<\/div>\n
<\/div>\n
\"homozygousmom\"<\/a><\/div>\n
<\/div>\n
This says if mom is homozygous, here allele1 is the same as her allele2. For those if Jon has null values in his FromMom column, then I skipped this step.<\/div>\n
<\/div>\n
\"homomomerror\"<\/a><\/div>\n
<\/div>\n
Clearly, I did mess this step from position one. As I was doing my previous steps, I thought that Jon’s results were very sparse.<\/div>\n
principle 2 fix<\/h5>\n

For this, I will again use the update query.<\/p>\n

\"homomomfix\"<\/a><\/p>\n

In this case, I didn’t bother writing ‘Is Null’ under the JonFromMom column. That is because even if there is something in there, I would just as soon overwrite it, as this is such a basic principle. I only missed 481,000 rows.<\/p>\n

second part of fix<\/h5>\n

Now that I have mom’s bases, I will go back and fill in Jon’s dad bases based on his mom bases. Those are also Principle 2 fillns where Jon is heterozygous. I don’t mind doing these updates in Access as they are so easy.<\/p>\n

\"dadsbasefrommomjon\"<\/a><\/p>\n

This says in the case where Jon is heterozygous and his mom has allele1, put Jon’s allele2 in as Jon’s allele from Dad. This query says if a Jon’s has allele1 from his Mom, the allele2\u00a0has to go to his dad.<\/p>\n

\"jonallele1fordad\"<\/a><\/p>\n

So that is an easy way to update over 7,000 rows in a few minutes.<\/p>\n

Next, On to Mom Patterns<\/h4>\n

It’s a good thing that I added these mom bases to Jon, because now it is time to look at mom patterns. From Athey:<\/p>\n

In the next step, we use the pattern on the mother\u2019s side to fill in as many more cells as possible. Finally, we can project the information in those newly filled cells back to the father\u2019s side using Principle 3 again. <\/em><\/p>\n

\u00a0This procedure will be the same one that I used for the Dad Patterns.<\/div>\n
aaab mom pattern<\/h5>\n
\u00a0I might as well go in alphabetical order. In this pattern, Jon will not match the other siblings.<\/div>\n
<\/div>\n
\"aaabmompattern\"<\/a><\/div>\n
<\/div>\n
This works, but it doesn’t include the areas where there are missing mom bases. So I will use it to get rough ID’s. There were about 45 AAAB Mom Patterns that I found. Perhaps the rough ID’s will do.<\/div>\n
AAAB Quality Control<\/h5>\n

My spreadsheet counts the numbers of ID’s between patterns.<\/p>\n

\"aaabqc\"<\/a><\/p>\n

619 is close to the cutoff that I had set. I went back to the original spreadsheet and found other AAAB patterns between the Stop and next Start. So I can combine those 2 AAAB Chromosome 15 patterns. I checked another pattern with about 700 ID’s from the Stop to the next AAAB Start. However, there was another pattern between, so those were a valid Stop and Start. There were about 45 AAAB Mom Patterns or about 2 per chromosome which seems like a lot.<\/p>\n

ABAA Mom Pattern<\/h5>\n

The query should be similar to the previous one. If Sharon isn’t the same as her siblings, we will have an ABAA Pattern.<\/p>\n

\"abaaqpattern\"<\/a><\/p>\n

This pattern was easier to figure out. There were about 35 of them.<\/p>\n

aaba Mom pattern<\/h5>\n

This is the one I should have done second if I had wanted to stay in alphabetical order. I checked a few with differences of about 500 between Stop and next Start, but they looked OK. There were a few single allele patterns.<\/p>\n

aabb mom pattern<\/h5>\n

I have 3 criteria for this one:<\/p>\n

\"aabbmompatternquery\"<\/a><\/p>\n

I had to enter that Sharon’s allele from mom could not be the same as Heidi’s allele from mom or I would get a lot of AAAA Patterns. When I looked for these, there appear to be 19 AABB maternal patterns.<\/p>\n

abab mom pattern<\/h5>\n

Again, this is a bit out of alphabetical order. This query is not unlike the previous one.<\/p>\n

\"ababq\"<\/a><\/p>\n

When I make Heidi’s mom base different from Sharon’s mom base, that gives me the ABAB pattern:<\/p>\n

\"ababresults\"<\/a><\/p>\n

Here I have Excel on the left where I am entering the results from the\u00a0Mom\u00a0Patterns that I found in Access.<\/p>\n

\"ababworksheet\"<\/a><\/p>\n

The jump in Chromosome 4 from position 6M to 37.9M indicates a change in pattern. That is entered in Excel on the left. The change from the previous pattern is shown as 7544 ID’s. ID’s should be the same as SNPs.<\/p>\n

A change in Chromosome is an obvious Stop and Start:<\/p>\n

\"ababex\"<\/a><\/p>\n

There were about 30 ABAB mom patterns for me and my 3 other siblings. I’ve done:<\/p>\n