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Local re-assembly and haplotype determination (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to re-assemble read data and determine candidate haplotypes as a prelude to variant calling. For more context information on how this fit...
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Difference between QUAL and GQ annotations in germline variant calling
It seems people often get confused about the difference between QUAL and GQ, so we hope this will clarify the difference. What it comes down to is that QUAL refers to the variant site whereas GQ r...
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How should I pre-process data from multiplexed sequencing and multi-library designs?
Our Best Practices pre-processing documentation assumes a simple experimental design in which you have one set of input sequence files (forward/reverse or interleaved FASTQ, or unmapped uBAM) per s...
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Jumping libraries
Jumping libraries are created to bypass difficult to align/map regions, such as those containing repetitive DNA sequences. Briefly, the DNA of interest is identified, cut into fragments either with...
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Bisulfite sequencing - Cytosine methylation
Cytosine methylation is a key component in epigenetic regulation of gene expression and frequently occurs at CpG sites throughout the genome. Bisulfite sequencing is a technique used to analyze the...
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Where can I find known variants, training and truth sets, and other resource files?
For general definitions of these terms, see this Dictionary entry. Humans If you're working with human data, you're in luck. We provide all resource files necessary for applying the Best Practice...
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How can I make GATK tools run faster?
It sure seems like everyone has a need for speed these days. So, there are two main ways to get your analysis results faster: Parallelism, which doesn't actually make the calculations faster, but...
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Missing physical phasing information in vcf?
The way the phasing algorithm decides to phase is by checking whether two variants always occur on the same haplotype or always occur on a different haplotypes. The excess haplotypes severely dilut...
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Evaluating the evidence for haplotypes and variant alleles (HaplotypeCaller and Mutect2)
This document details the procedure used by HaplotypeCaller to evaluate the evidence for variant alleles based on candidate haplotypes determined in the previous step for a given ActiveRegion. For ...
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SelectVariants Cookbook
How to use SelectVariants to find common variants: gatk SelectVariants \ -V gs://gatk-tutorials/workshop_1702/variant_discovery/data/inputVcfs/trio.vcf.gz \ -select 'vc.getGenotype("NA12...