verifyBamID verifies whether the reads in particular bam file match previously known genotypes for an individual (or a group of individuals). It also checks for sample swaps and cross-contaimination between samples.

There may be multiple versions of verifybamid available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail verifybamid 

To select a module use

module load verifybamid/[version]

where [version] is the version of choice.

verifybamid is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.

Environment variables set

• $PATH

References

• G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang. Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data. American Journal of Human Genetics 2012, 91:839-848. PubMed  |  PMC  |  Journal

Documentation

• Manual
• GitHub

Allocate an interactive session with sinteractive and use as follows

biowulf$ sinteractive 
node$ module load verifybamid
verifyBamID 1.1.3 -- verify identity and purity of sequence data
(c) 2010-2014 Hyun Min Kang, Goo Jun, and Goncalo Abecasis


Available Options
                             Input Files : --vcf [], --bam [], --bai [],
                                           --subset [], --smID []
                    VCF analysis options : --genoError [1.0e-03],
                                           --minAF [0.01],
                                           --minCallRate [0.50]
   Individuals to compare with chip data : --site, --self, --best
          Chip-free optimization options : --free-none, --free-mix [ON],
                                           --free-refBias, --free-full
          With-chip optimization options : --chip-none, --chip-mix [ON],
                                           --chip-refBias, --chip-full
                    BAM analysis options : --ignoreRG, --ignoreOverlapPair,
                                           --noEOF, --precise, --minMapQ [10],
                                           --maxDepth [20], --minQ [13],
                                           --maxQ [40], --grid [0.05]
                 Modeling Reference Bias : --refRef [1.00], --refHet [0.50],
                                           --refAlt [0.00]
                          Output options : --out [], --verbose
                               PhoneHome : --noPhoneHome,
                                           --phoneHomeThinning [50]

node$ verifyBamID --vcf input1.vcf --bam input1.bam --out output1 --verbose --ignoreRG
node$ exit
biowulf$

Create a batch script similar to the following example:

#! /bin/bash
# this file is verifybamid.sh

module load verifybamid || exit 1
verifyBamID --vcf input1.vcf --bam input1.bam --out output1 \
    --verbose --ignoreRG --noPhoneHome

Submit to the queue with sbatch:

biowulf$ sbatch verifybamid.sh

Create a swarm command file similar to the following example:

# this file is verifybamid.swarm
verifyBamID --vcf input1.vcf --bam input1.bam --out output1 --verbose --ignoreRG --noPhoneHome
verifyBamID --vcf input2.vcf --bam input2.bam --out output2 --verbose --ignoreRG --noPhoneHome
verifyBamID --vcf input3.vcf --bam input3.bam --out output3 --verbose --ignoreRG --noPhoneHome

And submit to the queue with swarm

biowulf$ swarm -f verifybamid.swarm