Changes

'''genotypeIdCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).

'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).

== Usage ==

== Usage ==

A key step in any genetic analysis is to verify whether data being generated matches expectations. This program checks whether reads in a BAM file match previous genotypes for a specific sample.  

A key step in any genetic analysis is to verify whether data being generated matches expectations. This program checks whether reads in a BAM file match previous genotypes for a specific sample.  

Using a mathematical model that relates observed sequence reads to an hypothetical true genotype, genotypeIdCheck tries to decide whether sequence reads match a particular individual or are more likely to be contaminated (including a small proportion of foreign DNA), derived from a closely related individual, or derived from a completely different individual.

Using a mathematical model that relates observed sequence reads to an hypothetical true genotype, bamGenotypeCheck tries to decide whether sequence reads match a particular individual or are more likely to be contaminated (including a small proportion of foreign DNA), derived from a closely related individual, or derived from a completely different individual.

== Basic Usage Example ==

== Basic Usage Example ==

Here is a typical command line:

Here is a typical command line:

   genotypeIDcheck -r /data/local/ref/karma.ref/human.g1k.v37.fa \

   bamGenotypeCheck -r /data/local/ref/karma.ref/human.g1k.v37.fa \

               -k BAMfiles.txt -p test.ped -d test.dat -m test.map

               -k BAMfiles.txt -p test.ped -d test.dat -m test.map

For each aligned base that overlaps a known genotype, we calculate the probability the probability that it was derived from a particular known genotype. This comparison considers only bases that overlap previously known genotypes and that meet the base quality and mapping quality thresholds.

For each aligned base that overlaps a known genotype, we calculate the probability the probability that it was derived from a particular known genotype. This comparison considers only bases that overlap previously known genotypes and that meet the base quality and mapping quality thresholds.

Each individual in a pedigree has a different combination of genotypes, and genotypeIdCheck will systematically search for the individual whose genotypes best match the observed read data.

Each individual in a pedigree has a different combination of genotypes, and bamGenotypeCheck will systematically search for the individual whose genotypes best match the observed read data.

For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]

For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]

== TODO ==

== TODO ==