Difference between revisions of "BamGenotypeCheck"

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'''LaneCheck'''
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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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<br>
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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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== Download bamGenotypeCheck  ==
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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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== Build bamGenotypeCheck  ==
 +
 
 +
Karma (which includes bamGenotypeCheck) is designed to be reasonably portable.
 +
 
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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 laneCheck&nbsp;works:
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Here is a typical command line:
  
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   lanecheck --referencegenome NCBI36.fa --dbSNPfile dbSNP.txt \
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   bamGenotypeCheck -r /data/local/ref/karma.ref/human.g1k.v37.fa \
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            --lanefile lane.lst --pedfile test.ped --datfile test.dat --mapfile test.map --prefix result
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              -k BAMfiles.txt -p test.ped -d test.dat -m test.map
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== Command Line Options ==
 
== Command Line Options ==
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=== Input Files ===
 
=== Input Files ===
  
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  --referencegenome ''referencegenome file''
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  -r  ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]''
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  --dbSNPfile      ''optional'' ''dbsnp position file, will provide more accurate background mismatch rate if excluding dbSNP positions''
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  -a  ''allele Frequency file in [[MERLIN format]]''
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  --lanefile        ''a list of lane file with path''
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  -p  ''pedigree file in [[MERLIN format]]''
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  --pedfile        ''genotype information of the samples for checking ''
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  -d ''data file in [[MERLIN format]]''
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  --datfile        ''a companion data file for pedigree file (each row: M snpname, e.g. M rs1234)''
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  -m  ''map file in [[MERLIN format]]''
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  --mapfile        ''a companion data file for pedigree file (each row: chr snpname pos, e.g. 5 rs1234 56789)''
 
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=== Basic Output Options ===
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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''
  
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--prefix ''specify the prefix name of the output file''
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=== Output Options ===
  
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=== Filtering&nbsp; ===
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-v  ''verbose output''
  
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  --minmapquality   ''reads with with mapquality falling below this threshold will be excluded''
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=== Filtering ===
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  --genocount      ''the maximum number of genotypes compared''  
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  --verbose        ''generate detailed''  
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  -b [int]   ''exclude bases with quality less than [int]''
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  --coverage
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  -M [int]  ''exclude reads with map quality less than [int]''
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--countbysite    ''generate detailed statistic for each base compared''
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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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  --memorymap ''use memory map technique for efficient memory sharing of reference genome file
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  -e [float] '' set minimum error base error to [float]''
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''
 
  
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== Principle of operation: ==
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== Principle of Operation ==
  
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The overall procedure is that the genotype identity checking program compares internal evidence from the sequence reads themselves to reference genotype information for a panel of candidate individuals. In the case of 1000 Genomes pilot data, these are HapMap genotypes from the same Coriell cell lines that are being sequenced. For each combination of [sequencing run x candidate individual] the program calculates the observed rate of mismatches at both "informative" and "background" locations and reports as "excess mismatch rate"
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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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            excess rate  =  (informative rate  -  background rate).
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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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"Informative" locations are those where the candidate individual is homozygous, according to the HapMap genotype information, and base calls are compared to the HapMap homozygous allele, rather than to the genome reference sequence. "Background" locations are all sites not known to be polymorphic and not recorded in dbSNP.
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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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<br>
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For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]
  
 
== TODO ==
 
== TODO ==
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Frequently, we will want to run lane checking on a mapped .bam file which already contains sequence data from many different instrument runs merged together. They are merged because the sequencing center said they all belong to the same individual. In Pilot 3, this was true for all of the Baylor LS 454 sequencing data. In this case, the read identifier in column 1 of the .sam file carries information about which sequencing run each read belongs to, as well as information that uniquely identifies that read within its run. The read identifiers often are dot or colon-separated strings of the form 'run_name&lt;sep&gt;read_number'. The 'run_name' may be either an SRR / ERR identifier or the sequencing center's own alpha-numeric internal run identifier.
 
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The "Read group classifier" is an extended regular expression such as '\(^[^.:]+\)[.:].*' which matches just the part of each read identifier that is common to all reads from one instrument run and which differs between instrument runs. The regular expression is passed into the lane checking program as an ascii string. The program keeps track of all distinct values it has seen for the matched portion, and must keep a separate tally of matches and mismatches for each combination of [read group x candidate individual]. By itself, the matched portion of each read identifier does not fully specify which original .fastq file a read came from. The 'bitwise flag' value in column 2 of the .sam format has the remaining information. This is able to distinguish between the 'left end', 'right end' and 'single end' reads which come from each Illumina paired-end sequencing run. The Baylor LS 454 data were all single end reads, so I did not have to deal with this complication.<br>
 
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<br>
 

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"