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GATK

GATK

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What is GATK?

GATK (Genome Analysis Toolkit) is a software package developed by the Broad Institute for variant discovery and genotype refinement in high-throughput sequencing data. It's widely used in genomic research and clinical settings to identify single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants from next-generation sequencing (NGS) data. The toolkit provides a comprehensive suite of tools for data preprocessing, variant calling, and variant filtering, following best practices for accuracy and reproducibility.

What other technologies are related to GATK?

GATK Complementary Technologies

BWA is a widely used alignment tool that generates BAM files which are a common input for GATK.
mentioned alongside GATK in 69% (413) of relevant job posts
Samtools provides utilities for manipulating alignments in the SAM and BAM formats, commonly used alongside GATK.
mentioned alongside GATK in 56% (331) of relevant job posts
Picard tools perform various pre-processing steps on sequencing data that are frequently used in conjunction with GATK for data preparation.
mentioned alongside GATK in 86% (128) of relevant job posts

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