was used for variant calling to estimate the SNP differences between these two variants [71, 72].
Single nucleotide variant and indel calls were generated using MuTect and GATK
To detect potential variants, we employed the Genome Analysis Toolkit (GATK
) to perform consensus calling, and the discovery pipeline is detailed in Figure S1.
The SNPs were called by using GATK
software under the criteria (Qual score [greater than or equal to] 30, QD < 20.0, ReadPosRankSum < -8.0, FS > 10.0 and QUAL < $MEANQUA).
Maverix continues to offer researchers a choice of alternative tools, including GATK
version 2.3 or FreeBayes for variant detection.
Former army chief-of-staff Oyay Deng Ajak(far left), with co-accused Pagan Amum Okiech, Majok D'Agot Atem and Ezekiel Lol Gatk
listen in court during their trial for treason (Photo: Charlton Doki/VOA)
In this perspective, we suggest using the UnifiedGenotyper module in the GATK
toolkit  for SNP discovery.
A detailed review of SNP-calling algorithms and challenges recommends recalibration of per-base quality scores (e.g., GATK
, SOAPsnp), use of an alignment algorithm with high sensitivity (e.g., Novo-align, Stampy), and SNP calling using Bayesian procedures or likelihood ratio tests and incorporation of linkage disequilibrium to improve SNP call accuracy .
GIS's regional research collaboration with Appistry builds upon Appistry's recent selection as the distributor for The Broad Institute's next generation Genome Analysis Tool Kit (GATK
), the world's most widely used software for data processing and variant calling of next-generation sequencing data.
Picard tools (http:// broadinstitute.github.io/picard/), SAMtools , and Genome Analysis Toolkit (GATK
)  were used for downstream processing and variant calling.
shtml), and GATK
Variants were called using genome analysis tool kit (GATK