Difference between revisions of "BamGenotypeCheck"

From Genome Analysis Wiki
Jump to navigationJump to search
 
(33 intermediate revisions by 4 users not shown)
Line 1: Line 1:
−
'''LaneCheck'''
+
{| style="width:100%; background:#FF8989; margin-top:1.2em; border:1px solid #ccc;" |
 +
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" |
 +
<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">This tool has been DEPRECATED, and replaced by [[VerifyBamID]]</div>
 +
|}
  
 +
'''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 ==
 +
 +
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 ==
 
== Basic Usage Example ==
  
−
Here is an example of how <code>glfTrio</code> works:
+
Here is a typical command line:
  
−
   lanecheck -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \
+
   bamGenotypeCheck  -r /data/local/ref/karma.ref/human.g1k.v37.fa \
−
          --father NA19239 --mother NA19238 --child NA19240 \
+
              -k BAMfiles.txt -p test.ped -d test.dat -m test.map
−
          --minMapQuality 30 --minTotalDepth 0 --maxTotalDepth 1000 \
 
−
          -b YRI.chrom20.SLX.vcf > YRI.chrom20.SLX.log
 
  
 
== Command Line Options ==
 
== Command Line Options ==
Line 16: Line 36:
 
=== Input Files ===
 
=== Input Files ===
  
−
  -f ''genotype likelihood file''   Father's [[GLF]]-format genotype likelihood file
+
-r  ''genome reference in [http://en.wikipedia.org/wiki/Fasta_format simplified FASTA format]''
−
  -m ''genotype likelihood file''   Mother's [[GLF]]-format genotype likelihood file
+
-a  ''allele Frequency file in [[MERLIN format]]''
−
  -c ''genotype likelihood file''    Child's [[GLF]]-format genotype likelihood file
+
-p  ''pedigree file in [[MERLIN format]]''
 +
-d  ''data file in [[MERLIN format]]''
 +
-m  ''map file in [[MERLIN format]]''
  
−
=== Basic Output Options ===
+
-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''
  
−
  -b ''baseCallFile''                Specifies the name of the output [[VCF]]-format base call file
+
=== Output Options ===
−
  -p ''threshold''                  The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''
 
−
  --reference                    Positions called as homozygous reference will be included in the output. 
 
−
  --verbose                      Print debug information to the screen
 
  
−
=== Filtering According to Depth and Map Quality ===
+
-v  ''verbose output''
  
−
  --minMapQuality ''threshold''      Positions where the root-means squared mapping quality falls below this threshold will be excluded.
+
=== Filtering ===
−
  --strict                      When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
 
−
                                before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
 
  
−
   --minTotalDepth ''threshold''           Positions where the read depth falls below this threshold will be excluded.
+
-b [int]   ''exclude bases with quality less than [int]''
−
   --maxTotalDepth ''threshold''           Positions where the read depth exceeds this threshold will be excluded.
+
-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)''
  
−
=== Sample Labels ===
+
=== Other Options ===
  
−
  --father ''fatherLabel''          Specifies a label for the male parent, which will be included in the output VCF file
+
-e [float] '' set minimum error base error to [float]''
−
  --mother ''motherLabel''          Specifies a label for the female parent, which will be included in the output VCF file
 
−
  --child ''childLabel''             Specifies a label for the child, which will be included in the output VCF file
 
  
−
=== X Chromosome Variant Calling ===
+
== Principle of Operation ==
  
−
  --xChr ''chromosomeName''          Label for the 'X' chromosome in the GLF file
+
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.
−
  --xStart ''sexChromosomeStart''    Start of the non-pseudo-autosomal portion of the X (2,709,521 bp in build 36)
 
−
  --xStop ''sexChromosomeEnd''      End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
 
  
−
Principle of operation:
+
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.
  
−
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"
+
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.
  
−
            excess rate  =  (informative rate  - background rate).
+
For more about the technical details, see the page [[Verifying Sample Identities - Implementation]]
  
−
"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.
 
−
                      abc
 
 
== 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"