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|Alternative name||Genotype Query Tools|
|Interface||Command line interface|
|Restrictions to use||None|
|Output data||The default output of GQT queries is VCF.|
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Publication for Genotype Query Tools
Comparative genomic analysis of esophageal squamous cell carcinoma between Asian and Caucasian patient populations
[…] 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 […]
Robust and rapid algorithms facilitate large scale whole genome sequencing downstream analysis in an integrative framework
[…] 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 […]
Novel bioinformatic developments for exome sequencing
[…] 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 […]
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