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Protocols

GQT specifications

Information


Unique identifier OMICS_08157
Name GQT
Alternative name Genotype Query Tools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Output data The default output of GQT queries is VCF.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Genotype Query Tools

GQT citations

 (3)
call_split

Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations

2017
Nat Commun
PMCID: 5688099
PMID: 29142225
DOI: 10.1038/s41467-017-01730-x
call_split See protocol

[…] for the mutual exclusivity between two patient populations using CoMEt, which uses a Markov chain Monte Carlo algorithm to compute the marginal probability of observing pairs of alterations. We used Genotype Query Tools to calculate the fixation index for each SNP site reported by the 1000 Genomes Project (phase 3) between southern Han Chinese (CHS) and the European super population (EUR). The SN […]

library_books

Robust and rapid algorithms facilitate large scale whole genome sequencing downstream analysis in an integrative framework

2017
Nucleic Acids Res
PMCID: 5435951
PMID: 28115622
DOI: 10.1093/nar/gkx019

[…] diseases.The bit-block algorithm provides an efficient way to store and represent genotypes in both hard disk and RAM. Compared with existing algorithms of binary encoding of genotypes (e.g. PLINK () GQT () and BGT () formats), our proposed algorithm has two unique features. First, it can flexibly encode both the phased and unphased genotypes with more than two alleles. In contrast, the existing a […]

library_books

Novel bioinformatic developments for exome sequencing

2016
Hum Genet
PMCID: 4883269
PMID: 27075447
DOI: 10.1007/s00439-016-1658-6

[…] ix format such as dbSNP (NCBI Resource Coordinators ) and Combined Annotation-Depended Depletion (CADD) scores (Kircher et al. ). Another option is to use the recently published Genotype Query Tools (GQT) to index and compress large number of VCF files. This tool also facilitates fast querying. GQT was used to compress the Exome Aggregation Consortium (ExAC) VCF file, consisting of 9.36 million ex […]

Citations

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GQT institution(s)
Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA

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