Difference between revisions of "BamGenotypeCheck"

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== Why genotypeIDcheck? ==
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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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When sequencing data arrives from the sequencer machines, several types of errors or contaminations can creep in.
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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).
  
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The most serious error that can occur is that the actual sample name for the sample gets swapped with a different sample.  In this case, what we think is one person's sequencing data is actually another.  Although they are confidential, in some cases, they are intended to be part of a family, and such an error causes problems in later analysis.
 
  
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Also, since we typically genotype the same samples along with running a full sequence of them, we want to know that the genotyping information matches the sequence, otherwise again, we will find errors in later analysis.
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== Download bamGenotypeCheck  ==
  
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Another set of problems occurs when the actual biological sample is contaminated in some way. It could be the case, for example, that certain common laboratory contaminates will be included in the sequencing data - knowing approximately how much of such contaminants exist (e.g. yeast) is useful.
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To get a copy go to the [http://csg.sph.umich.edu//pha/karma/download/ Karma Download] download page.
  
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So, the program genotypeIDcheck was written in order to discover if problems such as these exist, and if so, report them to the user.
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== Build bamGenotypeCheck  ==
  
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To work, genotypeIDcheck needs a) a list of sorted, calibrated BAM files to check, b) a genome reference to check against, c) a pedigree that describes the samples being checked.
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Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.  
  
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On output, genotypeIDcheck shows, for each read group in each BAM file, the individual in the pedigree that comes statistically closest to matching the reads in the read group, and the degree to how close that relationship is.  In addition, marker coverage of three different classes of markers is shown for that individual as well.
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However, since development occurs only on Ubuntu 9.10 x86 and x64 platforms, and later, there are likely other portability issues.
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We support Karma only on Ubuntu 9.10 and later on 64-bit processors.
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== Usage ==
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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.
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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 ==
  
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Here is an example of how genotypeIDcheck works:
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Here is a typical command line:
  
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   genotypeIDcheck -r /data/local/ref/karma.ref/human.g1k.v37.fa \
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   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
  
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=== Input Files ===
 
=== Input Files ===
  
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  -r  ''KARMA genome reference''
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  -r  ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]''
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  -k ''a filename that contains a list of BAM files to check''
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  -a ''allele Frequency file in [[MERLIN format]]''
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  -a ''pedigree Allele Frequency file''
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  -p ''pedigree file in [[MERLIN format]]''
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  -p ''pedigree .ped file''
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  -d ''data file in [[MERLIN format]]''
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  -d ''pedigree .dat file''
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  -m ''map file in [[MERLIN format]]''
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  -m ''pedigree .map file''
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-k  ''a list of BAM files to check''
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-c [int]  ''stop after reading [int] filtered sequence reads''
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  -C [int] ''stop after reading [int] reads, filtered or not''
  
 
=== Output Options ===
 
=== Output Options ===
  
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-c [int]  ''stop after reading [int] filtered sequence reads''
 
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-C [int]  ''stop after reading [int] reads, filtered or not''
 
 
  -v  ''verbose output''
 
  -v  ''verbose output''
  
 
=== Filtering ===
 
=== Filtering ===
  
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  -b [int] ''exclude marker positions with base quality less than [int]''
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  -b [int]   ''exclude bases with quality less than [int]''
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  -M [int] ''exclude all reads with map quality less than [int]''
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  -M [int]   ''exclude reads with map quality less than [int]''
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  -F [int] ''set custom BAM flags filter (not implemented at the moment)''
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-f [float] ''drop markers with minor allele frequency smaller than [float]''
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  -F [int]   ''set custom BAM flags filter (not implemented at the moment)''
  
 
=== Other Options ===
 
=== Other Options ===
  
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  -e [float] '' set minimum error estimate to [float]''
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  -e [float] '' set minimum error base error to [float]''
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== Principle of Operation ==
 
== Principle of Operation ==
  
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For computational and output purposes, we consider each read group sample in each BAM file to be distinct from all others.
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Each read group in a BAM file is evaluated independently. This means that in file with multiple read groups, problems will be flagged at the read group level (a plus). However, it also means that it might be hard to discern the correct assignment of read groups with very little data.
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For each aligned sample, we calculate the probability that the sample is from each individual in the pedigree according to five different probabilities of being identical by descent.  So from the base quality (again, assuming calibrated base qualities), the given base in the read, the marker corresponding reference base and genotype chip read data, you can compute the probability of that individual being the one in the sample for the given probability of IBD.
 
  
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What you actually want is the multiple of theses probabilities taken across all reads in the sample. This becomes impractically small, so we instead sum the logs of the probabilities.
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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.
  
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After the sample is read, the sample in the pedigree that contains the highest log-sum of computed Pibd values is assumed to have the strongest relationship to that sample.  The ID of the corresponding pedigree sample name is printed, the sample name indicated in the read group is printed, and coverage information is also printed.
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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.
  
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For more about the mathematical details, see the page [[Verifying Sample Identities - Implementation]]
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For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]
  
 
== TODO ==
 
== TODO ==

Latest revision as of 11:11, 2 February 2017

This tool has been DEPRECATED, and replaced by VerifyBamID

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 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

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, 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

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

Command Line Options

Input Files

-r  genome reference in simplified FASTA format
-a  allele Frequency file in MERLIN format
-p  pedigree file in MERLIN format
-d  data file in MERLIN format
-m  map file in MERLIN format

-k  a list of BAM files to check
-c [int]  stop after reading [int] filtered sequence reads
-C [int]  stop after reading [int] reads, filtered or not

Output Options

-v  verbose output

Filtering

-b [int]   exclude bases with quality less than [int]
-M [int]   exclude reads with map quality less than [int]
-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

-e [float]  set minimum error base error to [float]

Principle of Operation

Each read group in a BAM file is evaluated independently. This means that in file with multiple read groups, problems will be flagged at the read group level (a plus). However, it also means that it might be hard to discern the correct assignment of read groups with very little data.

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 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

TODO

Retrieved from "http://genome.sph.umich.edu/w/index.php?title=BamGenotypeCheck&oldid=14614"