Mapping 250K/500K SNP assay

chapter 7 | Analysis Workflow 205
3. Create column called “concordance check”. This column will
contain a 1 if the two genotype calls match and a 0 if they do not.
A. Enter the following formula “=IF(B2=C2,1,0)”.
B. Auto fill down the column.
4. Create a second Column Called “No Call”. This column will
contain “TRUE” if either call column contains a “NC”.
A. Enter the following formula “=OR(B2="NoCall",C2="NC")”.
B. Auto fill down the column.
5. Create a third column called “Valid Concordant SNP”. This column
will contain a “TRUE” if the SNP calls match and neither is a “NC”.
A. Enter the following formula “=AND(D2=1,E2=FALSE)”.
B. Auto fill down the column.
6. Count the number of SNPs that had a genotype call in both
experiments.
A. Within the spreadsheet, enter the following formula into a cell:
“=COUNTIF(E2:65536,"FALSE")”.
B. Press return.
7. Count the number of SNPs that have a genotype call in both
experiments and are concordant.
A. Elsewhere within the spreadsheet, enter the following formula
into a cell: “=COUNTIF(F2:65536,"TRUE")”.
B. Press return.
8. The Concordance rate can be calculated by dividing the value from
step 7 by the value from step 6.
The concordance rate should always be greater than 99%. Reasons
for a decline in the concordance rate include:
Selecting the wrong data set to compare to the reference DNA.
Contamination at some step in the assay.
Poor sample preparation.