VerifyBamID

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples.

Download verifyBamID

To get a copy go to the VerifyBamID Download download page.

Build verifyBamID

verifyBamID 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.

Currently we support verifyBamID only on Ubuntu 9.10 and later on 64-bit processors.

Basic Usage

A key step in any genetic analysis is to verify whether data being generated matches expectations. verifyBamID checks whether reads in a BAM file match previous genotypes for a specific sample. In addition, it detects possible sample mixture from population allele frequency only, which can be particularly useful when the genotype data is not available.

Using a mathematical model that relates observed sequence reads to an hypothetical true genotype, verifyBamID 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:

verifyBamID  --reference [reference.fa] --in [inputReads.bam] --bfile [inputGenotypes] --out [outPrefix] --verbose

where
[reference.fa] is a FASTA format file, preferably (but not necessarily) indexed a priori with karma or other libcsg-compatible software
[inputReads.bam] is a BAM (Binary Alignment Map) file of a sequence reads
[inputGenotypes] is input prefix of forward-stranded PLINK binary file
[outPrefix] is output prefix of output files - [outPrefix].{selfRG,selfSM,bestRG,bestSM} will be created.

More detailed description of command line input is provided below

Command Line Options

USAGE: 

  ./verifyBamID  [--ibdUnit <double>] [--mixUnit <double>] [-f <double>]
                 [-g <double>] [-d <integer>] [-m <integer>] [-Q
                 <integer>] [-q <integer>] [-B <string>] [-b <string>] [-l
                 <string>] -o <string> [-I <string>] [-s <string>] [-p
                 <string>] [-i <string>] -r <string> [-M] [-F] [-S] [-n]
                 [-v] [--] [--version] [-h]


Where: 

  --ibdUnit <double>
    unit of IBD values (default: 0.01)

  --mixUnit <double>
    unit of % mixture (default:0.01)

  -f <double>,  --minAF <double>
    Minimum allele frequency (default: 0.005). Markers with lower allele
    frequencies will be ignored

  -g <double>,  --genoError <double>
    Error rate in genotype data (default: 0.005)

  -d <integer>,  --maxDepth <integer>
    Maximum depth per site (default:20) - bases with higher depth will be
    ignored due to possible alignment artifacts. For deep coverage data,
    it is important to set this value to a sufficiently large number (e.g.
    200)

  -m <integer>,  --minMapQ <integer>
    Minimum mapping quality value (default:10) - reads with lower quality
    will be ignored

  -Q <integer>,  --maxQ <integer>
    Maximum Phred-scale base quality value (default:40) - higher base
    quality will be enforced to be this value

  -q <integer>,  --minQ <integer>
    Minimum Phred-scale base quality value (default:20) - bases with lower
    quality will be ignored

  -B <string>,  --bimpfile <string>
    PLINK format BIM file with allele frequency information at the last
    column

  -b <string>,  --bfile <string>
    Binary PLINK format genotype file prefix. Must be forward-stranded

  -l <string>,  --log <string>
    Log file - default: [out].log

  -o <string>,  --out <string>
    (required)  Prefix of output files

  -I <string>,  --index <string>
    Index of input BAM file - [inputBam].bai will be default value

  -s <string>,  --insuffix <string>
    Suffix of input BAM file for multi-chromosome inputs

  -p <string>,  --inprefix <string>
    Prefix of input BAM file for multi-chromosome inputs

  -i <string>,  --in <string>
    Input BAM file. Must be sorted and indexed

  -r <string>,  --reference <string>
    (required)  Karma's reference sequence

  -M,  --mmap
    toggle whether to use memory map (default:true)

  -F,  --bimAF
    use the allele frequency information by loading .bimp file instead of
    .bim file

  -S,  --selfonly
    compare the genotypes with SELF (annotated sample) only (default:off)

  -n,  --noeof
    Do not check EOF marker for BAM file (default:off)

  -v,  --verbose
    Toggle verbose mode (default:off)

  --,  --ignore_rest
    Ignores the rest of the labeled arguments following this flag.

  --version
    Displays version information and exits.

  -h,  --help
    Displays usage information and exits.

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