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'''genotypeIdCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">This tool has been DEPRECATED, and replaced by [[VerifyBamID]]</div>
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'''bamGenotypeCheck''' is a program that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals).
== Download bamGenotypeCheck ==
To get a copy go to the [http://csg.sph.umich.edu//pha/karma/download/ Karma Download] download page.
== Build bamGenotypeCheck ==
Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.
However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, and later, there are likely other portability issues.
We support Karma only on Ubuntu 9.10 and later on 64-bit processors.
== 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:
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
=== Input Files ===
=== Input Files ===
-r ''FASTA format genome reference''
-r ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]''
-a ''allele Frequency file''
-a ''allele Frequency file in [[MERLIN format]]''
-p ''pedigree file in [[MERLIN format]]''
-p ''pedigree file in [[MERLIN format]]''
-d ''data file in [[MERLIN format]]''
-d ''data file in [[MERLIN format]]''
=== Filtering ===
=== Filtering ===
-b [int] ''exclude bases with quality less than [int]''
-b [int] ''exclude bases with quality less than [int]''
-M [int] ''exclude reads with map quality less than [int]''
-M [int] ''exclude reads with map quality less than [int]''
-F [int] ''set custom BAM flags filter (not implemented at the moment)''
-f [float] ''drop markers with minor allele frequency smaller than [float]''
-F [int] ''set custom BAM flags filter (not implemented at the moment)''
=== Other Options ===
=== Other Options ===
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 ==
