Changes

If we have a list of bases that overlap a known genotype, we can calculate the probability of a match or mismatch at each base as:  

If we have a list of bases that overlap a known genotype, we can calculate the probability of a match or mismatch at each base as:  

{| width="200" cellspacing="1" cellpadding="1" border="1" summary="Summary of Variables Used Below"

{| width="100%" cellspacing="1" cellpadding="1" border="1" summary="Summary of Variables Used Below"

|+ Notation

|+ Notation  

|-

|-

| Variable

| Variable  

| Definition

| Definition

|-

|-

| A/A

| A/A  

| Previously known genotype; we only consider homozygous sites.

| Previously known genotype; we only consider homozygous sites.

|-

|-

| <math>P_A</math>

| <span class="texhtml">''P''_''A''</span>  

| Frequency of allele A in the population

| Frequency of allele A in the population

|-

|-

| <math>P_{ibd}</math>

| <span class="texhtml">''P''_{''i''''b''''d''}</span>  

| Probability that the sequenced sample and the target sample share a chromosome. This should be 1.0 when we have sequenced the correct sample and 0.0 if we sequence an unrelated sample. If we sequence a related sample (e.g. a parent or sibling of the target sample), we will see intermediate values.

| Probability that the sequenced sample and the target sample share a chromosome. This should be 1.0 when we have sequenced the correct sample and 0.0 if we sequence an unrelated sample. If we sequence a related sample (e.g. a parent or sibling of the target sample), we will see intermediate values.

|-

|-

| <math>\{epsilon}</math>

| <math>\epsilon</math>

| Estimate error rate for the current base in the sequence data.

| Estimate error rate for the current base in the sequence data.

|}

|}