BamGenotypeCheck

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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