cleanCall

Correcting for DNA contamination in genotype calling

Quick Start

git clone https://github.com/hyunminkang/cleancall.git
cd cleancall
./configure --prefix [/path/to/install]
make
make install
[/path/to/install]/cctools pileup --loci [in.sites.vcf.gz] \\
     --index [index.file.with.sample.id.and.bam.file.txt] \\
     --out [output.pileup] --ref [ref.fa] --run [num.parallel.jobs]
[/path/to/install]/cctools verify --index [output.pileup.ped] \\
     --out [output.verify] --vcf [in.sites.vcf.gz] \\
     --run [num.parallel.jobs]
[/path/to/install]/cctools genotype --invcf [in.sites.vcf.gz] \\
     --ped [output.verify.ped] --out [output.genotype.vcf.gz] \\
     --ref [ref.fa] --run [num.parallel.jobs]

Introduction

cleanCall is a software package for detecting, estimating, correcting for contamination in DNA sequence data. It contains one C++ program, cleanCall, as a core binary file that runs statistical algorithms. It contains three wrapper scripts, cctools-pileup for producing pileups from sequence data, cctools-verify for detecting and estimating contamination, and cctools-genotype for correcting for contaminations. These wrapper scripts allows to run cleanCall across a large number of sequenced genomes or exomes in a highly parallel manner.

Detailed Usage

The basic usage can be obtained by simply typing the command without any argument (e.g. cctools-genotype). More detailed usage can be obtained with -man option (e.g. cctools-genotype -man). If you have questions about cleanCall, you may send me an email at hmkang@umich.edu

Citing cleanCall

G Jun, M Flickinger, KN Hetrick, JM Romm, KF Doheny, GR Abecasis, M Boehnke (2012) Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data, The American Journal of Human Genetics 91 (5), 839-848

Frequently Asked Questions (FAQs)

(in construction..)

MrFlick / cleancall